Last updated: 2015-12-11

Code version: 884b335605607bd2cf5c9a1ada1e345466388866

Objective

Previously, we compared normalized coefficient of variations across individuals. Here, we will also compare the mean gene expression across individuals, using single cell sequencing data and bulk RNA-seq data.

It would be interesting to learn the possible overlap or non-overlap between the genes that we observed significant individual differences in coefficient of variations versus those different in mean gene expression levels across cells.

From here on we will work with the filtered data without NA19098.r2.

Set up

library("data.table")
library("dplyr")
library("limma")
library("edgeR")
library("ggplot2")
library("grid")
theme_set(theme_bw(base_size = 12))
source("functions.R")

Prepare data

Input annotation of only QC-filtered single cells. Remove NA19098.r2

anno_qc_filter <- read.table("../data/annotation-filter.txt", header = TRUE,
                   stringsAsFactors = FALSE)

Import endogeneous gene molecule counts that are QC-filtered, CPM-normalized, ERCC-normalized, and also processed to remove unwanted variation from batch effet. ERCC genes are removed from this file.

molecules_ENSG <- read.table("../data/molecules-final.txt", header = TRUE, stringsAsFactors = FALSE)

Input moleclule counts before log2 CPM transformation. This file is used to compute percent zero-count cells per sample.

molecules_sparse <- read.table("../data/molecules-filter.txt", header = TRUE, stringsAsFactors = FALSE)

molecules_sparse <- molecules_sparse[grep("ENSG", rownames(molecules_sparse)), ]
stopifnot( all.equal(rownames(molecules_ENSG), rownames(molecules_sparse)) )

Normalize coefficient of variation

Compute coefficient of variation.

# Compute CV and mean of normalized molecule counts (take 2^(log2-normalized count))

molecules_cv_batch_ENSG <- 
  lapply(1:length(unique(anno_qc_filter$batch)), function(per_batch) {
      molecules_per_batch <- 2^molecules_ENSG[ , unique(anno_qc_filter$batch) == unique(anno_qc_filter$batch)[per_batch] ]
      mean_per_gene <- apply(molecules_per_batch, 1, mean, na.rm = TRUE)
      sd_per_gene <- apply(molecules_per_batch, 1, sd, na.rm = TRUE)
      cv_per_gene <- data.frame(mean = mean_per_gene,
                                sd = sd_per_gene,
                                cv = sd_per_gene/mean_per_gene)
      rownames(cv_per_gene) <- rownames(molecules_ENSG)
  
      # cv_per_gene <- cv_per_gene[rowSums(is.na(cv_per_gene)) == 0, ]
      cv_per_gene$batch <- unique(anno_qc_filter$batch)[per_batch]
      
      # Add sparsity percent
      molecules_sparse_per_batch <- molecules_sparse[ , unique(anno_qc_filter$batch) == unique(anno_qc_filter$batch)[per_batch]]
      cv_per_gene$sparse <- rowMeans(as.matrix(molecules_sparse_per_batch) == 0)
        
      return(cv_per_gene)
      }) 
names(molecules_cv_batch_ENSG) <- unique(anno_qc_filter$batch)

Merge summary data.frames.

df_ENSG <- do.call(rbind, molecules_cv_batch_ENSG)

Compute rolling medians across all samples.

library(zoo)
# Compute a data-wide coefficient of variation on CPM normalized counts.
data_cv_ENSG <- apply(2^molecules_ENSG, 1, sd)/apply(2^molecules_ENSG, 1, mean)

# Order of genes by mean expression levels
order_gene <- order(apply(2^molecules_ENSG, 1, mean))

# Rolling medians of log10 squared CV by mean expression levels
roll_medians <- rollapply(log10(data_cv_ENSG^2)[order_gene], width = 50, by = 25,
                         FUN = median, fill = list("extend", "extend", "NA") )
ii_na <- which( is.na(roll_medians) )
roll_medians[ii_na] <- median( log10(data_cv_ENSG^2)[order_gene][ii_na] )

names(roll_medians) <- rownames(molecules_ENSG)[order_gene]


# re-order rolling medians
reorder_gene <- match(rownames(molecules_ENSG), names(roll_medians) )
roll_medians <- roll_medians[ reorder_gene ]

stopifnot( all.equal(names(roll_medians), rownames(molecules_ENSG) ) )

Compute adjusted coefficient of variation.

# adjusted coefficient of variation on log10 scale
log10cv2_adj_ENSG <- 
  lapply(1:length(molecules_cv_batch_ENSG), function(per_batch) {
    foo <- log10(molecules_cv_batch_ENSG[[per_batch]]$cv^2) - roll_medians
    return(foo)
})
df_ENSG$log10cv2_adj_ENSG <- do.call(c, log10cv2_adj_ENSG)

Compare coefficients of variations

library(limma)

df_limma <- matrix(df_ENSG$log10cv2_adj_ENSG, 
                      nrow = nrow(molecules_ENSG), ncol = 8, byrow = FALSE)

design <- data.frame(individual = factor(rep(unique(anno_qc_filter$individual), each = 3) ),
                     rep = factor(rep(c(1:3), times = 3)) )
design <- design[ with(design, !(individual == "NA19098" & rep == "2")), ]

colnames(df_limma) <- with(design, paste0(individual, rep))

fit_limma <- lmFit(df_limma, design = model.matrix( ~ individual, data = design))                      
fit_limma <- eBayes(fit_limma)

False discovery control adjustment.

F.p.adj <- p.adjust(fit_limma$F.p.value, method = "fdr")

Cutoffs

df_cuts <- data.frame(cuts = c(.001, .01, .05, .1, .15, .2))
df_cuts$sig_count <- sapply(1:6, function(per_cut) {
                    sum(F.p.adj < df_cuts$cuts[per_cut] )
                    })
df_cuts
   cuts sig_count
1 0.001        91
2 0.010       192
3 0.050       385
4 0.100       560
5 0.150       780
6 0.200      1004

False discovery control adjutment.

F.p.adj <- p.adjust(fit_limma$F.p.value, method = "fdr")

Squared CV vs. mean expression level

We plotted out per gene average CVs across samples versus average expression level for the endogeneous genes, and identified the genes classifed as significantly different between individuals in coefficients of variation.

df_compare <- 
  data.frame(mean = rowMeans( as.matrix( 
                      do.call(cbind, lapply(molecules_cv_batch_ENSG, "[[", 1) ) ) ),
             cv2 = rowMeans( as.matrix( 
                      do.call(cbind, lapply(molecules_cv_batch_ENSG, "[[", 3) ) )^2 ),
             adj_cv2 = rowMeans( 10^as.matrix( 
                      do.call(cbind, log10cv2_adj_ENSG) ) ) )
             
library(broman)
crayon <- brocolors("crayons")
par(mar=c(5,5,3,1))
with(df_compare, plot(x = log10(mean), y = cv2, pch = 1, cex = 1, col = "grey50",
                      lwd = .5,
                      ylab = "average squared coeffcient of variations \n across samples",
                      xlab = "log10 average of mean CPM across samples") )
with(df_compare[F.p.adj < .2, ], points(x = log10(mean), y = cv2, pch = 16, cex = .6,
                                        col = crayon["Tumbleweed"]) )
with(df_compare[F.p.adj < .1, ], points(x = log10(mean), y = cv2, pch = 16, cex = .6,
                                        col = crayon["Orange"]) )
with(df_compare[F.p.adj < .01, ], points(x = log10(mean), y = cv2, pch = 16, cex = .6,
                                        col = crayon["Scarlet"]) )
title(main = "Avg. Squred CV vs. log10(Avg. mean count)")
legend("topright", pch = c(1, 16, 16, 16), 
       legend = c("All genes", "Adj p-value < .2", 
                  "Adj p-value < .1", "Adj p-value < .01"),
       col = c("grey50", crayon[c("Tumbleweed", "Orange", "Scarlet")]),
       bty = "n")

par(mar=c(5,5,3,1))
with(df_compare, plot(x = log10(mean), y = adj_cv2, pch = 1, cex = 1, col = "grey50",
                      lwd = .5,
                      ylab = "average squared coeffcient of variations \n across samples",
                      xlab = "log10 average of mean CPM across samples") )
with(df_compare[F.p.adj < .2, ], points(x = log10(mean), y = adj_cv2, pch = 16, cex = .6,
                                        col = crayon["Tumbleweed"]) )
with(df_compare[F.p.adj < .1, ], points(x = log10(mean), y = adj_cv2, pch = 16, cex = .6,
                                        col = crayon["Orange"]) )
with(df_compare[F.p.adj < .01, ], points(x = log10(mean), y = adj_cv2, pch = 16, cex = .6,
                                        col = crayon["Scarlet"]) )
title(main = "Avg. Adjusted Squred CV vs. log10(Avg. mean count)")
legend("topright", pch = c(1, 16, 16, 16), 
       legend = c("All genes", "Adj p-value < .2", 
                  "Adj p-value < .1", "Adj p-value < .01"),
       col = c("grey50", crayon[c("Tumbleweed", "Orange", "Scarlet")]),
       bty = "n")

Investigate…

Our naive analysis seems to pick up genes with different density between individuals.

library(gridExtra)
order_low_cv <- order(df_compare[F.p.adj < .01, ]$cv)
low_plots <- lapply(1:6, function(i) {
  ind <- order_low_cv[i]
  ggplot(data.frame(values = unlist(molecules_ENSG[ind, ]),
                    individual = factor(anno_qc_filter$individual),
                    replicate = factor(anno_qc_filter$replicate),
                    batch = factor(anno_qc_filter$batch), check.rows = F), 
         aes(x = values)) + 
    geom_density(aes(group = batch, col = individual)) + 
    ggtitle(paste(rownames(molecules_ENSG)[ind],
                  ";CV = ", round(df_compare[F.p.adj < .01, ]$cv[ind], 2) ) )
})
grid.arrange(grobs = low_plots, ncol = 2)

order_high_cv <- order(df_compare[F.p.adj < .01, ]$cv, decreasing = TRUE)
high_plots <- lapply(1:6, function(i) {
  ind <- order_high_cv[i]
  ggplot(data.frame(values = unlist(molecules_ENSG[ind, ]),
                    individual = factor(anno_qc_filter$individual),
                    replicate = factor(anno_qc_filter$replicate),
                    batch = factor(anno_qc_filter$batch), check.rows = F), 
         aes(x = values)) + 
    geom_density(aes(group = batch, col = individual)) + 
    ggtitle(paste(rownames(molecules_ENSG)[ind],
                  ";CV = ", round(df_compare[F.p.adj < .01, ]$cv[ind], 2) ) )
})
grid.arrange(grobs = high_plots, ncol = 2)

Annotation

ENSEMBLE database

sig_cv <- order(F.p.adj)[F.p.adj < .05]
library("biomaRt")
ensembl <- useMart(host = "grch37.ensembl.org",
                   biomart = "ENSEMBL_MART_ENSEMBL",
                   dataset = "hsapiens_gene_ensembl")

differential_CV_genes_info <- getBM(attributes = c("ensembl_gene_id", "chromosome_name",
                                                   "external_gene_name", "transcript_count",
                                                   "description"),
                                    filters = "ensembl_gene_id",
                                    values = rownames(molecules_ENSG[sig_cv, ]),
                                    mart = ensembl)
differential_CV_genes_info
    ensembl_gene_id chromosome_name external_gene_name transcript_count
1   ENSG00000006432              14             MAP3K9                6
2   ENSG00000008018               6              PSMB1                2
3   ENSG00000008311               7               AASS                7
4   ENSG00000008988               8              RPS20               11
5   ENSG00000010072               1              SPRTN                6
6   ENSG00000011021               1              CLCN6                9
7   ENSG00000011114              14              BTBD7                9
8   ENSG00000013561               5              RNF14               18
9   ENSG00000029725              17             RABEP1               10
10  ENSG00000030419               2              IKZF2               17
11  ENSG00000033170              14               FUT8               17
12  ENSG00000050393               6              MCUR1                4
13  ENSG00000051825              12           MPHOSPH9               26
14  ENSG00000060339              10              CCAR1               18
15  ENSG00000062485              12                 CS               33
16  ENSG00000063177              19              RPL18               16
17  ENSG00000064995               6              TAF11                2
18  ENSG00000065548               2             ZC3H15               10
19  ENSG00000066136               1               NFYC               24
20  ENSG00000068400               X            GRIPAP1                9
21  ENSG00000069943              15               PIGB               12
22  ENSG00000070756               8             PABPC1               23
23  ENSG00000071054               2             MAP4K4               18
24  ENSG00000073111               3               MCM2                9
25  ENSG00000075234              22              TTC38                7
26  ENSG00000076382              17              SPAG5               16
27  ENSG00000076706              11               MCAM               18
28  ENSG00000077713               X           SLC25A43                5
29  ENSG00000078967               7             UBE2D4               12
30  ENSG00000079215               5             SLC1A3               14
31  ENSG00000079277               1              MKNK1               30
32  ENSG00000079739               1               PGM1                5
33  ENSG00000080371              12              RAB21                4
34  ENSG00000081692               1              JMJD4                5
35  ENSG00000085733              11               CTTN               16
36  ENSG00000087008               4              ACOX3                8
37  ENSG00000087157              17               PGS1               16
38  ENSG00000088035               1               ALG6                7
39  ENSG00000090060              14             PAPOLA               25
40  ENSG00000090971              19              NAT14                5
41  ENSG00000091039              12             OSBPL8               17
42  ENSG00000092330              14              TINF2               16
43  ENSG00000093144               6             ECHDC1               24
44  ENSG00000097021               1              ACOT7               11
45  ENSG00000099139               9              PCSK5                5
46  ENSG00000100106              22             TRIOBP               11
47  ENSG00000100129              22              EIF3L               13
48  ENSG00000100139              22            MICALL1                6
49  ENSG00000100296              22              THOC5               17
50  ENSG00000100629              14             CEP128               17
51  ENSG00000100644              14              HIF1A               12
52  ENSG00000100784              14            RPS6KA5                7
53  ENSG00000100908              14               EMC9                7
54  ENSG00000100916              14             BRMS1L                7
55  ENSG00000101189              20              MRGBP                1
56  ENSG00000101194              20            SLC17A9                7
57  ENSG00000101198              20             NKAIN4                9
58  ENSG00000101333              20              PLCB4               14
59  ENSG00000101493              18             ZNF516                6
60  ENSG00000101596              18             SMCHD1               14
61  ENSG00000101974               X             ATP11C               11
62  ENSG00000101997               X             CCDC22                3
63  ENSG00000102054               X              RBBP7               12
64  ENSG00000102078               X           SLC25A14               14
65  ENSG00000102158               X              MAGT1                3
66  ENSG00000102189              12               EEA1                5
67  ENSG00000102226               X              USP11               12
68  ENSG00000102531              13             FNDC3A                6
69  ENSG00000102901              16              CENPT               36
70  ENSG00000103316              16               CRYM               12
71  ENSG00000103356              16              EARS2               17
72  ENSG00000103449              16              SALL1                6
73  ENSG00000103544              16           C16orf62               25
74  ENSG00000103978              15            TMEM87A               13
75  ENSG00000104497               8              SNX16               11
76  ENSG00000104611               8             SH2D4A                6
77  ENSG00000104885              19              DOT1L               11
78  ENSG00000105325              19               FZR1                8
79  ENSG00000105520              19      DKFZP761J1410                8
80  ENSG00000106236               7              NPTX2                2
81  ENSG00000106785               9             TRIM14                7
82  ENSG00000107021               9            TBC1D13                5
83  ENSG00000108010              10              GLRX3                5
84  ENSG00000108176              10            DNAJC12                5
85  ENSG00000108384              17             RAD51C               17
86  ENSG00000108774              17              RAB5C                9
87  ENSG00000109255               4                NMU                6
88  ENSG00000109576               4              AADAT                8
89  ENSG00000109670               4              FBXW7               13
90  ENSG00000109689               4              STIM2               13
91  ENSG00000110046              11              ATG2A                6
92  ENSG00000110063              11               DCPS                3
93  ENSG00000110074              11            FOXRED1               19
94  ENSG00000110422              11              HIPK3                6
95  ENSG00000110514              11               MADD               22
96  ENSG00000111087              12               GLI1                8
97  ENSG00000111215              12               PRR4               22
98  ENSG00000111271              12             ACAD10               25
99  ENSG00000111450              12               STX2                4
100 ENSG00000111670              12             GNPTAB               10
101 ENSG00000111911               6              HINT3                1
102 ENSG00000112081               6              SRSF3                3
103 ENSG00000112305               6              SMAP1                6
104 ENSG00000112699               6               GMDS               10
105 ENSG00000112715               6              VEGFA               25
106 ENSG00000113758               5               DBN1               12
107 ENSG00000114388               3              NPRL2               17
108 ENSG00000114784               3              EIF1B                4
109 ENSG00000115539               2              PDCL3                3
110 ENSG00000115738               2                ID2                4
111 ENSG00000115841               2              RMDN2               12
112 ENSG00000116285               1             ERRFI1                5
113 ENSG00000116641               1              DOCK7                8
114 ENSG00000116704               1            SLC35D1                2
115 ENSG00000116991               1            SIPA1L2                6
116 ENSG00000117020               1               AKT3               10
117 ENSG00000117280               1             RAB7L1                9
118 ENSG00000118200               1            CAMSAP2                6
119 ENSG00000118564               4              FBXL5               14
120 ENSG00000119599              14              DCAF4               15
121 ENSG00000119686              14             FLVCR2               13
122 ENSG00000119866               2             BCL11A               12
123 ENSG00000120053              10               GOT1                4
124 ENSG00000120526               8             NUDCD1                4
125 ENSG00000120756               3               PLS1               12
126 ENSG00000121057              17              AKAP1               18
127 ENSG00000121644               1              DESI2                4
128 ENSG00000121680              11              PEX16               11
129 ENSG00000123066              12             MED13L               10
130 ENSG00000123179              13               EBPL                8
131 ENSG00000123219               5              CENPK               17
132 ENSG00000123384              12               LRP1               12
133 ENSG00000123643               5            SLC36A1               10
134 ENSG00000123933               4               MXD4                5
135 ENSG00000124145              20               SDC4                2
136 ENSG00000124493               6               GRM4               14
137 ENSG00000124508               6             BTN2A2               16
138 ENSG00000125398              17               SOX9                1
139 ENSG00000125449              17              ARMC7                5
140 ENSG00000125505              19             MBOAT7               14
141 ENSG00000125686              17               MED1                5
142 ENSG00000125817              20              CENPB                1
143 ENSG00000125845              20               BMP2                1
144 ENSG00000126107               1             HECTD3                7
145 ENSG00000126790              14            L3HYPDH                9
146 ENSG00000126858              17              RHOT1               17
147 ENSG00000127125               1               PPCS                9
148 ENSG00000129055               3            ANAPC13                6
149 ENSG00000129317              12              PUS7L                8
150 ENSG00000129353              19            SLC44A2               15
151 ENSG00000130340               6               SNX9                1
152 ENSG00000130559               9            CAMSAP1               10
153 ENSG00000130764               1             LRRC47                3
154 ENSG00000131149              16               GSE1               12
155 ENSG00000131153              16              GINS2                3
156 ENSG00000131876              15             SNRPA1               15
157 ENSG00000132405               4            TBC1D14                9
158 ENSG00000132475              17              H3F3B               13
159 ENSG00000132561               8              MATN2               18
160 ENSG00000132846               5              ZBED3                3
161 ENSG00000133169               X               BEX1                1
162 ENSG00000133226               1              SRRM1               24
163 ENSG00000133243              19              BTBD2               10
164 ENSG00000133313              18              CNDP2               29
165 ENSG00000134049              18            IER3IP1                1
166 ENSG00000134198               1             TSPAN2                5
167 ENSG00000134247               1             PTGFRN                3
168 ENSG00000134318               2              ROCK2                8
169 ENSG00000134363               5                FST                5
170 ENSG00000135272               7              MDFIC                7
171 ENSG00000135473              12               PAN2               20
172 ENSG00000135486              12            HNRNPA1               14
173 ENSG00000136261               7               BZW2               13
174 ENSG00000136536               2             MARCH7                9
175 ENSG00000136560               2               TANK               24
176 ENSG00000136717               2               BIN1               14
177 ENSG00000136868               9            SLC31A1                3
178 ENSG00000137040               9             RANBP6                2
179 ENSG00000137331               6               IER3                2
180 ENSG00000137364               6               TPMT                1
181 ENSG00000137947               1              GTF2B                7
182 ENSG00000138018               2               EPT1                4
183 ENSG00000138107              10             ACTR1A                8
184 ENSG00000138622              15               HCN4                1
185 ENSG00000138944              22           KIAA1644                1
186 ENSG00000139679              13              LPAR6                8
187 ENSG00000140395              15              WDR61               16
188 ENSG00000140830              16             TXNL4B                6
189 ENSG00000140832              16           MARVELD3                6
190 ENSG00000140905              16               GCSH                6
191 ENSG00000140941              16           MAP1LC3B               10
192 ENSG00000140988              16               RPS2               17
193 ENSG00000141002              16              TCF25               24
194 ENSG00000141738              17               GRB7               15
195 ENSG00000142065              19              ZFP14                2
196 ENSG00000142168              21               SOD1                4
197 ENSG00000142530              19            FAM71E1                6
198 ENSG00000142541              19             RPL13A               12
199 ENSG00000142634               1              EFHD2                2
200 ENSG00000143320               1             CRABP2                3
201 ENSG00000143353               1            LYPLAL1               12
202 ENSG00000143776               1           CDC42BPA               15
203 ENSG00000144034               2              TPRKB               10
204 ENSG00000144233               2           AMMECR1L                2
205 ENSG00000144401               2           METTL21A               13
206 ENSG00000144711               3             IQSEC1                5
207 ENSG00000144827               3             ABHD10                6
208 ENSG00000145016               3           KIAA0226               11
209 ENSG00000145293               4             ENOPH1                3
210 ENSG00000145632               5               PLK2               14
211 ENSG00000145730               5                PAM               29
212 ENSG00000145912               5               NHP2                6
213 ENSG00000146350               6            TBC1D32                9
214 ENSG00000146433               6            TMEM181                1
215 ENSG00000146856               7              AGBL3                9
216 ENSG00000147027               X             TMEM47                1
217 ENSG00000147394               X             ZNF185               12
218 ENSG00000147416               8           ATP6V1B2                6
219 ENSG00000147854               9              UHRF2               13
220 ENSG00000147905               9             ZCCHC7                9
221 ENSG00000148297               9              MED22               10
222 ENSG00000148300               9              REXO4                6
223 ENSG00000148337               9               CIZ1               27
224 ENSG00000148399               9               DPH7               14
225 ENSG00000148908              10              RGS10                5
226 ENSG00000149131              11           SERPING1               12
227 ENSG00000149743              11              TRPT1               16
228 ENSG00000150471               4              LPHN3               19
229 ENSG00000151413              14              NUBPL               14
230 ENSG00000152904               1              GGPS1                9
231 ENSG00000152939               5           MARVELD2                6
232 ENSG00000153989               6               NUS1                1
233 ENSG00000154545               X             MAGED4               11
234 ENSG00000154556               4             SORBS2               65
235 ENSG00000154620               Y             TMSB4Y                1
236 ENSG00000155393              16             HEATR3                6
237 ENSG00000155975               8             VPS37A               12
238 ENSG00000156931               3               VPS8               27
239 ENSG00000157014               3             TATDN2                4
240 ENSG00000157823              15              AP3S2               15
241 ENSG00000157837              12              SPPL3                9
242 ENSG00000157851               2             DPYSL5                6
243 ENSG00000158006               1             PAFAH2                7
244 ENSG00000158079               9             PTPDC1                3
245 ENSG00000158864               1             NDUFS2               16
246 ENSG00000159202              17              UBE2Z                8
247 ENSG00000159459              15               UBR1               12
248 ENSG00000160075               1              SSU72                4
249 ENSG00000160131               X              VMA21                3
250 ENSG00000160214              21               RRP1                7
251 ENSG00000160551              17              TAOK1                6
252 ENSG00000160584              11               SIK3               17
253 ENSG00000161551              19             ZNF577               17
254 ENSG00000161958              17              FGF11                6
255 ENSG00000161996              16              WDR90               25
256 ENSG00000162231              11               NXF1               18
257 ENSG00000162576               1              MXRA8               10
258 ENSG00000162616               1             DNAJB4                6
259 ENSG00000162836               1               ACP6                6
260 ENSG00000162998               2               FRZB                1
261 ENSG00000163125               1              RPRD2                5
262 ENSG00000163362               1           C1orf106                7
263 ENSG00000163428               3             LRRC58                1
264 ENSG00000163482               2              STK36               17
265 ENSG00000163584               3            RPL22L1                6
266 ENSG00000163704               3              PRRT3                3
267 ENSG00000163930               3               BAP1               10
268 ENSG00000163947               3            ARHGEF3               15
269 ENSG00000164056               4              SPRY1                6
270 ENSG00000164081               3             TEX264               14
271 ENSG00000164117               4              FBXO8                4
272 ENSG00000164163               4              ABCE1               10
273 ENSG00000164663               6              USP49                8
274 ENSG00000164764               8             SBSPON                2
275 ENSG00000164933               8           SLC25A32                6
276 ENSG00000165169               X             DYNLT3                3
277 ENSG00000165275               9            TRMT10B                9
278 ENSG00000165630              10             PRPF18                3
279 ENSG00000165916              11              PSMC3               12
280 ENSG00000166426              15             CRABP1                3
281 ENSG00000166704              19             ZNF606               10
282 ENSG00000166888              12              STAT6               24
283 ENSG00000167118               9               URM1                6
284 ENSG00000167302              17             ENTHD2               13
285 ENSG00000167306              18              MYO5B                8
286 ENSG00000167380              19             ZNF226               19
287 ENSG00000167654              19              ATCAY                8
288 ENSG00000168040              11               FADD                1
289 ENSG00000168872              16             DDX19A               16
290 ENSG00000169021              19            UQCRFS1                1
291 ENSG00000169169              19              CPT1C               25
292 ENSG00000169814               3                BTD               12
293 ENSG00000169905               1           TOR1AIP2                6
294 ENSG00000169908               3             TM4SF1                4
295 ENSG00000169951              16             ZNF764                3
296 ENSG00000170266               3               GLB1               20
297 ENSG00000170448               4              NFXL1                8
298 ENSG00000170871               4           KIAA0232                5
299 ENSG00000171161               1             ZNF672                7
300 ENSG00000171310              12             CHST11                6
301 ENSG00000171700              20              RGS19                4
302 ENSG00000171861              17             RNMTL1                4
303 ENSG00000172167               8               MTBP                8
304 ENSG00000172717              14             FAM71D               10
305 ENSG00000173465              11             SSSCA1                7
306 ENSG00000173486              11              FKBP2                6
307 ENSG00000173744               2              AGFG1                8
308 ENSG00000173926               5             MARCH3                5
309 ENSG00000174456              12           C12orf76                8
310 ENSG00000174695               5           TMEM167A                6
311 ENSG00000175130               1           MARCKSL1                1
312 ENSG00000175215              12             CTDSP2                8
313 ENSG00000175279               1             APITD1                7
314 ENSG00000177105              11               RHOG                4
315 ENSG00000177119              12               ANO6                8
316 ENSG00000177600              11              RPLP2                8
317 ENSG00000177879               5              AP3S1                8
318 ENSG00000179943              19               FIZ1                5
319 ENSG00000179958              16             DCTPP1                5
320 ENSG00000180822               6              PSMG4               10
321 ENSG00000181827              15               RFX7                6
322 ENSG00000181830              11            SLC35C1                5
323 ENSG00000181915              10                ADO                1
324 ENSG00000182919              11           C11orf54               14
325 ENSG00000182986              19             ZNF320               14
326 ENSG00000183530              22             PRR14L                9
327 ENSG00000183864              22               TOB2                2
328 ENSG00000184007               1             PTP4A2               20
329 ENSG00000184348               6          HIST1H2AK                1
330 ENSG00000185215              14            TNFAIP2               13
331 ENSG00000185420               1              SMYD3               19
332 ENSG00000185684              12            EP400NL               14
333 ENSG00000185721              22               DRG1                6
334 ENSG00000185722              17             ANKFY1               14
335 ENSG00000186635              11              ARAP1               21
336 ENSG00000186716              22                BCR               16
337 ENSG00000187140               1              FOXD3                1
338 ENSG00000187193              16               MT1X                4
339 ENSG00000187514               2               PTMA               12
340 ENSG00000188690              10               UROS               10
341 ENSG00000189334               1            S100A14                6
342 ENSG00000196374               6          HIST1H2BM                1
343 ENSG00000196648              15          GOLGA6L20                4
344 ENSG00000197102              14            DYNC1H1               11
345 ENSG00000197183              20          C20orf112                9
346 ENSG00000197459               6          HIST1H2BH                1
347 ENSG00000197879              17              MYO1C               21
348 ENSG00000198176              13              TFDP1                9
349 ENSG00000198315               6            ZKSCAN8                4
350 ENSG00000198393              12              ZNF26                6
351 ENSG00000198464              19             ZNF480                6
352 ENSG00000198589               4               LRBA               14
353 ENSG00000198612               2              COPS8                8
354 ENSG00000198887               9               SMC5                3
355 ENSG00000198917               9           C9orf114                5
356 ENSG00000198960               X             ARMCX6                8
357 ENSG00000203930               X          LINC00632                5
358 ENSG00000204071               X             TCEAL6                2
359 ENSG00000204356               6              NELFE               13
360 ENSG00000204442              13            FAM155A                1
361 ENSG00000204536               6             CCHCR1               30
362 ENSG00000204568               6            MRPS18B                5
363 ENSG00000205138              19             SDHAF1                1
364 ENSG00000205476              14            CCDC85C                7
365 ENSG00000205572               5             SERF1B                8
366 ENSG00000205659              14              LIN52                5
367 ENSG00000205937              16              RNPS1               26
368 ENSG00000213024              19              NUP62               24
369 ENSG00000213614              15               HEXA               18
370 ENSG00000213762              19             ZNF134                4
371 ENSG00000215114               8             UBXN2B                5
372 ENSG00000221909               7            FAM200A                2
373 ENSG00000225921               6               NOL7                3
374 ENSG00000228474               2               OST4                3
375 ENSG00000229644              10             NAMPTL                2
376 ENSG00000240849              20            TMEM189                6
377 ENSG00000242612              16              DECR2               12
378 ENSG00000247626               2              MARS2                1
379 ENSG00000254858              19            MPV17L2                4
380 ENSG00000255103               1           KIAA0754                1
381 ENSG00000256525              17              POLG2               10
382 ENSG00000257315               1              ZBED6                1
383 ENSG00000261052              16            SULT1A3               13
384 ENSG00000264364              17             DYNLL2                1
385 ENSG00000269404              19               SPIB                8
                                                                                                                      description
1                                                  mitogen-activated protein kinase kinase kinase 9 [Source:HGNC Symbol;Acc:6861]
2                                             proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]
3                                                               aminoadipate-semialdehyde synthase [Source:HGNC Symbol;Acc:17366]
4                                                                            ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]
5                                                                      SprT-like N-terminal domain [Source:HGNC Symbol;Acc:25356]
6                                                             chloride channel, voltage-sensitive 6 [Source:HGNC Symbol;Acc:2024]
7                                                                    BTB (POZ) domain containing 7 [Source:HGNC Symbol;Acc:18269]
8                                                                           ring finger protein 14 [Source:HGNC Symbol;Acc:10058]
9                                                  rabaptin, RAB GTPase binding effector protein 1 [Source:HGNC Symbol;Acc:17677]
10                                                            IKAROS family zinc finger 2 (Helios) [Source:HGNC Symbol;Acc:13177]
11                                            fucosyltransferase 8 (alpha (1,6) fucosyltransferase) [Source:HGNC Symbol;Acc:4019]
12                                                     mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]
13                                                                         M-phase phosphoprotein 9 [Source:HGNC Symbol;Acc:7215]
14                                                   cell division cycle and apoptosis regulator 1 [Source:HGNC Symbol;Acc:24236]
15                                                                                 citrate synthase [Source:HGNC Symbol;Acc:2422]
16                                                                           ribosomal protein L18 [Source:HGNC Symbol;Acc:10310]
17                TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa [Source:HGNC Symbol;Acc:11544]
18                                                             zinc finger CCCH-type containing 15 [Source:HGNC Symbol;Acc:29528]
19                                                            nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]
20                                                                      GRIP1 associated protein 1 [Source:HGNC Symbol;Acc:18706]
21                                         phosphatidylinositol glycan anchor biosynthesis, class B [Source:HGNC Symbol;Acc:8959]
22                                                           poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
23                                          mitogen-activated protein kinase kinase kinase kinase 4 [Source:HGNC Symbol;Acc:6866]
24                                                   minichromosome maintenance complex component 2 [Source:HGNC Symbol;Acc:6944]
25                                                              tetratricopeptide repeat domain 38 [Source:HGNC Symbol;Acc:26082]
26                                                                      sperm associated antigen 5 [Source:HGNC Symbol;Acc:13452]
27                                                                  melanoma cell adhesion molecule [Source:HGNC Symbol;Acc:6934]
28                                                             solute carrier family 25, member 43 [Source:HGNC Symbol;Acc:30557]
29                                                   ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]
30                   solute carrier family 1 (glial high affinity glutamate transporter), member 3 [Source:HGNC Symbol;Acc:10941]
31                                                 MAP kinase interacting serine/threonine kinase 1 [Source:HGNC Symbol;Acc:7110]
32                                                                             phosphoglucomutase 1 [Source:HGNC Symbol;Acc:8905]
33                                                               RAB21, member RAS oncogene family [Source:HGNC Symbol;Acc:18263]
34                                                                     jumonji domain containing 4 [Source:HGNC Symbol;Acc:25724]
35                                                                                        cortactin [Source:HGNC Symbol;Acc:3338]
36                                                                    acyl-CoA oxidase 3, pristanoyl [Source:HGNC Symbol;Acc:121]
37                                                         phosphatidylglycerophosphate synthase 1 [Source:HGNC Symbol;Acc:30029]
38                                                             ALG6, alpha-1,3-glucosyltransferase [Source:HGNC Symbol;Acc:23157]
39                                                                        poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]
40                                                 N-acetyltransferase 14 (GCN5-related, putative) [Source:HGNC Symbol;Acc:28918]
41                                                                oxysterol binding protein-like 8 [Source:HGNC Symbol;Acc:16396]
42                                                       TERF1 (TRF1)-interacting nuclear factor 2 [Source:HGNC Symbol;Acc:11824]
43                                                         enoyl CoA hydratase domain containing 1 [Source:HGNC Symbol;Acc:21489]
44                                                                         acyl-CoA thioesterase 7 [Source:HGNC Symbol;Acc:24157]
45                                                    proprotein convertase subtilisin/kexin type 5 [Source:HGNC Symbol;Acc:8747]
46                                                                TRIO and F-actin binding protein [Source:HGNC Symbol;Acc:17009]
47                                           eukaryotic translation initiation factor 3, subunit L [Source:HGNC Symbol;Acc:18138]
48                                                                                    MICAL-like 1 [Source:HGNC Symbol;Acc:29804]
49                                                                                   THO complex 5 [Source:HGNC Symbol;Acc:19074]
50                                                                      centrosomal protein 128kDa [Source:HGNC Symbol;Acc:20359]
51          hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) [Source:HGNC Symbol;Acc:4910]
52                                               ribosomal protein S6 kinase, 90kDa, polypeptide 5 [Source:HGNC Symbol;Acc:10434]
53                                                           ER membrane protein complex subunit 9 [Source:HGNC Symbol;Acc:20273]
54                                                      breast cancer metastasis-suppressor 1-like [Source:HGNC Symbol;Acc:20512]
55                                                                      MRG/MORF4L binding protein [Source:HGNC Symbol;Acc:15866]
56                           solute carrier family 17 (vesicular nucleotide transporter), member 9 [Source:HGNC Symbol;Acc:16192]
57                                                        Na+/K+ transporting ATPase interacting 4 [Source:HGNC Symbol;Acc:16191]
58                                                                          phospholipase C, beta 4 [Source:HGNC Symbol;Acc:9059]
59                                                                         zinc finger protein 516 [Source:HGNC Symbol;Acc:28990]
60                        structural maintenance of chromosomes flexible hinge domain containing 1 [Source:HGNC Symbol;Acc:29090]
61                                                                      ATPase, class VI, type 11C [Source:HGNC Symbol;Acc:13554]
62                                                                coiled-coil domain containing 22 [Source:HGNC Symbol;Acc:28909]
63                                                                 retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]
64                              solute carrier family 25 (mitochondrial carrier, brain), member 14 [Source:HGNC Symbol;Acc:10984]
65                                                                         magnesium transporter 1 [Source:HGNC Symbol;Acc:28880]
66                                                                         early endosome antigen 1 [Source:HGNC Symbol;Acc:3185]
67                                                                 ubiquitin specific peptidase 11 [Source:HGNC Symbol;Acc:12609]
68                                                       fibronectin type III domain containing 3A [Source:HGNC Symbol;Acc:20296]
69                                                                            centromere protein T [Source:HGNC Symbol;Acc:25787]
70                                                                                   crystallin, mu [Source:HGNC Symbol;Acc:2418]
71                                                       glutamyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:29419]
72                                                               spalt-like transcription factor 1 [Source:HGNC Symbol;Acc:10524]
73                                                             chromosome 16 open reading frame 62 [Source:HGNC Symbol;Acc:24641]
74                                                                       transmembrane protein 87A [Source:HGNC Symbol;Acc:24522]
75                                                                                sorting nexin 16 [Source:HGNC Symbol;Acc:14980]
76                                                                        SH2 domain containing 4A [Source:HGNC Symbol;Acc:26102]
77                                                       DOT1-like histone H3K79 methyltransferase [Source:HGNC Symbol;Acc:24948]
78                                             fizzy/cell division cycle 20 related 1 (Drosophila) [Source:HGNC Symbol;Acc:24824]
79                                   Lipid phosphate phosphatase-related protein type 2  [Source:UniProtKB/Swiss-Prot;Acc:Q96GM1]
80                                                                            neuronal pentraxin II [Source:HGNC Symbol;Acc:7953]
81                                                                  tripartite motif containing 14 [Source:HGNC Symbol;Acc:16283]
82                                                                   TBC1 domain family, member 13 [Source:HGNC Symbol;Acc:25571]
83                                                                                  glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]
84                                                    DnaJ (Hsp40) homolog, subfamily C, member 12 [Source:HGNC Symbol;Acc:28908]
85                                                                                  RAD51 paralog C [Source:HGNC Symbol;Acc:9820]
86                                                                RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]
87                                                                                     neuromedin U [Source:HGNC Symbol;Acc:7859]
88                                                                   aminoadipate aminotransferase [Source:HGNC Symbol;Acc:17929]
89                            F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:16712]
90                                                                  stromal interaction molecule 2 [Source:HGNC Symbol;Acc:19205]
91                                                                            autophagy related 2A [Source:HGNC Symbol;Acc:29028]
92                                                                     decapping enzyme, scavenger [Source:HGNC Symbol;Acc:29812]
93                                                FAD-dependent oxidoreductase domain containing 1 [Source:HGNC Symbol;Acc:26927]
94                                                         homeodomain interacting protein kinase 3 [Source:HGNC Symbol;Acc:4915]
95                                                               MAP-kinase activating death domain [Source:HGNC Symbol;Acc:6766]
96                                                                         GLI family zinc finger 1 [Source:HGNC Symbol;Acc:4317]
97                                                                       proline rich 4 (lacrimal) [Source:HGNC Symbol;Acc:18020]
98                                                        acyl-CoA dehydrogenase family, member 10 [Source:HGNC Symbol;Acc:21597]
99                                                                                       syntaxin 2 [Source:HGNC Symbol;Acc:3403]
100                           N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits [Source:HGNC Symbol;Acc:29670]
101                                                   histidine triad nucleotide binding protein 3 [Source:HGNC Symbol;Acc:18468]
102                                                         serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]
103                                                                                 small ArfGAP 1 [Source:HGNC Symbol;Acc:19651]
104                                                                     GDP-mannose 4,6-dehydratase [Source:HGNC Symbol;Acc:4369]
105                                                           vascular endothelial growth factor A [Source:HGNC Symbol;Acc:12680]
106                                                                                       drebrin 1 [Source:HGNC Symbol;Acc:2695]
107                                             nitrogen permease regulator-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24969]
108                                                    eukaryotic translation initiation factor 1B [Source:HGNC Symbol;Acc:30792]
109                                                                               phosducin-like 3 [Source:HGNC Symbol;Acc:28860]
110                          inhibitor of DNA binding 2, dominant negative helix-loop-helix protein [Source:HGNC Symbol;Acc:5361]
111                                                            regulator of microtubule dynamics 2 [Source:HGNC Symbol;Acc:26567]
112                                                             ERBB receptor feedback inhibitor 1 [Source:HGNC Symbol;Acc:18185]
113                                                                     dedicator of cytokinesis 7 [Source:HGNC Symbol;Acc:19190]
114                          solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1 [Source:HGNC Symbol;Acc:20800]
115                                               signal-induced proliferation-associated 1 like 2 [Source:HGNC Symbol;Acc:23800]
116                                                    v-akt murine thymoma viral oncogene homolog 3 [Source:HGNC Symbol;Acc:393]
117                                                         RAB7, member RAS oncogene family-like 1 [Source:HGNC Symbol;Acc:9789]
118                              calmodulin regulated spectrin-associated protein family, member 2 [Source:HGNC Symbol;Acc:29188]
119                                                        F-box and leucine-rich repeat protein 5 [Source:HGNC Symbol;Acc:13602]
120                                                              DDB1 and CUL4 associated factor 4 [Source:HGNC Symbol;Acc:20229]
121                            feline leukemia virus subgroup C cellular receptor family, member 2 [Source:HGNC Symbol;Acc:20105]
122                                                  B-cell CLL/lymphoma 11A (zinc finger protein) [Source:HGNC Symbol;Acc:13221]
123                                                    glutamic-oxaloacetic transaminase 1, soluble [Source:HGNC Symbol;Acc:4432]
124                                                                       NudC domain containing 1 [Source:HGNC Symbol;Acc:24306]
125                                                                                       plastin 1 [Source:HGNC Symbol;Acc:9090]
126                                                                 A kinase (PRKA) anchor protein 1 [Source:HGNC Symbol;Acc:367]
127                                                                   desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]
128                                                                peroxisomal biogenesis factor 16 [Source:HGNC Symbol;Acc:8857]
129                                                               mediator complex subunit 13-like [Source:HGNC Symbol;Acc:22962]
130                                                                  emopamil binding protein-like [Source:HGNC Symbol;Acc:18061]
131                                                                           centromere protein K [Source:HGNC Symbol;Acc:29479]
132                                              low density lipoprotein receptor-related protein 1 [Source:HGNC Symbol;Acc:6692]
133                               solute carrier family 36 (proton/amino acid symporter), member 1 [Source:HGNC Symbol;Acc:18761]
134                                                                     MAX dimerization protein 4 [Source:HGNC Symbol;Acc:13906]
135                                                                                     syndecan 4 [Source:HGNC Symbol;Acc:10661]
136                                                              glutamate receptor, metabotropic 4 [Source:HGNC Symbol;Acc:4596]
137                                                            butyrophilin, subfamily 2, member A2 [Source:HGNC Symbol;Acc:1137]
138                                                           SRY (sex determining region Y)-box 9 [Source:HGNC Symbol;Acc:11204]
139                                                                  armadillo repeat containing 7 [Source:HGNC Symbol;Acc:26168]
140                                           membrane bound O-acyltransferase domain containing 7 [Source:HGNC Symbol;Acc:15505]
141                                                                      mediator complex subunit 1 [Source:HGNC Symbol;Acc:9234]
142                                                                     centromere protein B, 80kDa [Source:HGNC Symbol;Acc:1852]
143                                                                    bone morphogenetic protein 2 [Source:HGNC Symbol;Acc:1069]
144                                           HECT domain containing E3 ubiquitin protein ligase 3 [Source:HGNC Symbol;Acc:26117]
145                                                        L-3-hydroxyproline dehydratase (trans-) [Source:HGNC Symbol;Acc:20488]
146                                                                   ras homolog family member T1 [Source:HGNC Symbol;Acc:21168]
147                                                         phosphopantothenoylcysteine synthetase [Source:HGNC Symbol;Acc:25686]
148                                                          anaphase promoting complex subunit 13 [Source:HGNC Symbol;Acc:24540]
149                                        pseudouridylate synthase 7 homolog (S. cerevisiae)-like [Source:HGNC Symbol;Acc:25276]
150                                       solute carrier family 44 (choline transporter), member 2 [Source:HGNC Symbol;Acc:17292]
151                                                                                sorting nexin 9 [Source:HGNC Symbol;Acc:14973]
152                                             calmodulin regulated spectrin-associated protein 1 [Source:HGNC Symbol;Acc:19946]
153                                                              leucine rich repeat containing 47 [Source:HGNC Symbol;Acc:29207]
154                                                                       Gse1 coiled-coil protein [Source:HGNC Symbol;Acc:28979]
155                                                          GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]
156                                                 small nuclear ribonucleoprotein polypeptide A' [Source:HGNC Symbol;Acc:11152]
157                                                                  TBC1 domain family, member 14 [Source:HGNC Symbol;Acc:29246]
158                                                                   H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]
159                                                                                      matrilin 2 [Source:HGNC Symbol;Acc:6908]
160                                                             zinc finger, BED-type containing 3 [Source:HGNC Symbol;Acc:20711]
161                                                                     brain expressed, X-linked 1 [Source:HGNC Symbol;Acc:1036]
162                                                            serine/arginine repetitive matrix 1 [Source:HGNC Symbol;Acc:16638]
163                                                                  BTB (POZ) domain containing 2 [Source:HGNC Symbol;Acc:15504]
164                                               CNDP dipeptidase 2 (metallopeptidase M20 family) [Source:HGNC Symbol;Acc:24437]
165                                               immediate early response 3 interacting protein 1 [Source:HGNC Symbol;Acc:18550]
166                                                                                  tetraspanin 2 [Source:HGNC Symbol;Acc:20659]
167                                                             prostaglandin F2 receptor inhibitor [Source:HGNC Symbol;Acc:9601]
168                                        Rho-associated, coiled-coil containing protein kinase 2 [Source:HGNC Symbol;Acc:10252]
169                                                                                     follistatin [Source:HGNC Symbol;Acc:3971]
170                                                        MyoD family inhibitor domain containing [Source:HGNC Symbol;Acc:28870]
171                             PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20074]
172                                                      heterogeneous nuclear ribonucleoprotein A1 [Source:HGNC Symbol;Acc:5031]
173                                                          basic leucine zipper and W2 domains 2 [Source:HGNC Symbol;Acc:18808]
174                         membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17393]
175                                                   TRAF family member-associated NFKB activator [Source:HGNC Symbol;Acc:11562]
176                                                                           bridging integrator 1 [Source:HGNC Symbol;Acc:1052]
177                                        solute carrier family 31 (copper transporter), member 1 [Source:HGNC Symbol;Acc:11016]
178                                                                           RAN binding protein 6 [Source:HGNC Symbol;Acc:9851]
179                                                                      immediate early response 3 [Source:HGNC Symbol;Acc:5392]
180                                                                 thiopurine S-methyltransferase [Source:HGNC Symbol;Acc:12014]
181                                                                general transcription factor IIB [Source:HGNC Symbol;Acc:4648]
182                                   ethanolaminephosphotransferase 1 (CDP-ethanolamine-specific) [Source:HGNC Symbol;Acc:29361]
183                                 ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) [Source:HGNC Symbol;Acc:167]
184                        hyperpolarization activated cyclic nucleotide-gated potassium channel 4 [Source:HGNC Symbol;Acc:16882]
185                                                                                       KIAA1644 [Source:HGNC Symbol;Acc:29335]
186                                                               lysophosphatidic acid receptor 6 [Source:HGNC Symbol;Acc:15520]
187                                                                            WD repeat domain 61 [Source:HGNC Symbol;Acc:30300]
188                                                                            thioredoxin-like 4B [Source:HGNC Symbol;Acc:26041]
189                                                                     MARVEL domain containing 3 [Source:HGNC Symbol;Acc:30525]
190                                         glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]
191                                            microtubule-associated protein 1 light chain 3 beta [Source:HGNC Symbol;Acc:13352]
192                                                                           ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]
193                                               transcription factor 25 (basic helix-loop-helix) [Source:HGNC Symbol;Acc:29181]
194                                                          growth factor receptor-bound protein 7 [Source:HGNC Symbol;Acc:4567]
195                                                                      ZFP14 zinc finger protein [Source:HGNC Symbol;Acc:29312]
196                                                                superoxide dismutase 1, soluble [Source:HGNC Symbol;Acc:11179]
197                                                  family with sequence similarity 71, member E1 [Source:HGNC Symbol;Acc:25107]
198                                                                         ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]
199                                                               EF-hand domain family, member D2 [Source:HGNC Symbol;Acc:28670]
200                                                        cellular retinoic acid binding protein 2 [Source:HGNC Symbol;Acc:2339]
201                                                                       lysophospholipase-like 1 [Source:HGNC Symbol;Acc:20440]
202                                                  CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737]
203                                                                         TP53RK binding protein [Source:HGNC Symbol;Acc:24259]
204                                                                                   AMMECR1-like [Source:HGNC Symbol;Acc:28658]
205                                                                     methyltransferase like 21A [Source:HGNC Symbol;Acc:30476]
206                                                                     IQ motif and Sec7 domain 1 [Source:HGNC Symbol;Acc:29112]
207                                                               abhydrolase domain containing 10 [Source:HGNC Symbol;Acc:25656]
208                                                                                       KIAA0226 [Source:HGNC Symbol;Acc:28991]
209                                                                          enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]
210                                                                             polo-like kinase 2 [Source:HGNC Symbol;Acc:19699]
211                                                   peptidylglycine alpha-amidating monooxygenase [Source:HGNC Symbol;Acc:8596]
212                                                                         NHP2 ribonucleoprotein [Source:HGNC Symbol;Acc:14377]
213                                                                  TBC1 domain family, member 32 [Source:HGNC Symbol;Acc:21485]
214                                                                      transmembrane protein 181 [Source:HGNC Symbol;Acc:20958]
215                                                                 ATP/GTP binding protein-like 3 [Source:HGNC Symbol;Acc:27981]
216                                                                       transmembrane protein 47 [Source:HGNC Symbol;Acc:18515]
217                                                           zinc finger protein 185 (LIM domain) [Source:HGNC Symbol;Acc:12976]
218                                       ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 [Source:HGNC Symbol;Acc:854]
219                 ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12557]
220                                                          zinc finger, CCHC domain containing 7 [Source:HGNC Symbol;Acc:26209]
221                                                                    mediator complex subunit 22 [Source:HGNC Symbol;Acc:11477]
222                                                REX4, RNA exonuclease 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:12820]
223                                                       CDKN1A interacting zinc finger protein 1 [Source:HGNC Symbol;Acc:16744]
224                                                                     diphthamide biosynthesis 7 [Source:HGNC Symbol;Acc:25199]
225                                                             regulator of G-protein signaling 10 [Source:HGNC Symbol;Acc:9992]
226                                    serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 [Source:HGNC Symbol;Acc:1228]
227                                                                      tRNA phosphotransferase 1 [Source:HGNC Symbol;Acc:20316]
228                                                                                  latrophilin 3 [Source:HGNC Symbol;Acc:20974]
229                                                                nucleotide binding protein-like [Source:HGNC Symbol;Acc:20278]
230                                                           geranylgeranyl diphosphate synthase 1 [Source:HGNC Symbol;Acc:4249]
231                                                                     MARVEL domain containing 2 [Source:HGNC Symbol;Acc:26401]
232                          nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]
233                                                                   melanoma antigen family D, 4 [Source:HGNC Symbol;Acc:23793]
234                                                             sorbin and SH3 domain containing 2 [Source:HGNC Symbol;Acc:24098]
235                                                                      thymosin beta 4, Y-linked [Source:HGNC Symbol;Acc:11882]
236                                                                       HEAT repeat containing 3 [Source:HGNC Symbol;Acc:26087]
237                                          vacuolar protein sorting 37 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24928]
238                                             vacuolar protein sorting 8 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29122]
239                                                                 TatD DNase domain containing 2 [Source:HGNC Symbol;Acc:28988]
240                                               adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]
241                                                                signal peptide peptidase like 3 [Source:HGNC Symbol;Acc:30424]
242                                                                     dihydropyrimidinase-like 5 [Source:HGNC Symbol;Acc:20637]
243                                             platelet-activating factor acetylhydrolase 2, 40kDa [Source:HGNC Symbol;Acc:8579]
244                                               protein tyrosine phosphatase domain containing 1 [Source:HGNC Symbol;Acc:30184]
245               NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7708]
246                                                               ubiquitin-conjugating enzyme E2Z [Source:HGNC Symbol;Acc:25847]
247                                             ubiquitin protein ligase E3 component n-recognin 1 [Source:HGNC Symbol;Acc:16808]
248                                SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]
249                                               VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:22082]
250                                                                     ribosomal RNA processing 1 [Source:HGNC Symbol;Acc:18785]
251                                                                                   TAO kinase 1 [Source:HGNC Symbol;Acc:29259]
252                                                                            SIK family kinase 3 [Source:HGNC Symbol;Acc:29165]
253                                                                        zinc finger protein 577 [Source:HGNC Symbol;Acc:28673]
254                                                                     fibroblast growth factor 11 [Source:HGNC Symbol;Acc:3667]
255                                                                            WD repeat domain 90 [Source:HGNC Symbol;Acc:26960]
256                                                                     nuclear RNA export factor 1 [Source:HGNC Symbol;Acc:8071]
257                                                                 matrix-remodelling associated 8 [Source:HGNC Symbol;Acc:7542]
258                                                    DnaJ (Hsp40) homolog, subfamily B, member 4 [Source:HGNC Symbol;Acc:14886]
259                                                           acid phosphatase 6, lysophosphatidic [Source:HGNC Symbol;Acc:29609]
260                                                                        frizzled-related protein [Source:HGNC Symbol;Acc:3959]
261                                             regulation of nuclear pre-mRNA domain containing 2 [Source:HGNC Symbol;Acc:29039]
262                                                            chromosome 1 open reading frame 106 [Source:HGNC Symbol;Acc:25599]
263                                                              leucine rich repeat containing 58 [Source:HGNC Symbol;Acc:26968]
264                                                                     serine/threonine kinase 36 [Source:HGNC Symbol;Acc:17209]
265                                                                   ribosomal protein L22-like 1 [Source:HGNC Symbol;Acc:27610]
266                                                           proline-rich transmembrane protein 3 [Source:HGNC Symbol;Acc:26591]
267                                BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) [Source:HGNC Symbol;Acc:950]
268                                                   Rho guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:683]
269                                    sprouty homolog 1, antagonist of FGF signaling (Drosophila) [Source:HGNC Symbol;Acc:11269]
270                                                                           testis expressed 264 [Source:HGNC Symbol;Acc:30247]
271                                                                                F-box protein 8 [Source:HGNC Symbol;Acc:13587]
272                                               ATP-binding cassette, sub-family E (OABP), member 1 [Source:HGNC Symbol;Acc:69]
273                                                                ubiquitin specific peptidase 49 [Source:HGNC Symbol;Acc:20078]
274                                     somatomedin B and thrombospondin, type 1 domain containing [Source:HGNC Symbol;Acc:30362]
275                             solute carrier family 25 (mitochondrial folate carrier), member 32 [Source:HGNC Symbol;Acc:29683]
276                                                              dynein, light chain, Tctex-type 3 [Source:HGNC Symbol;Acc:11694]
277                                            tRNA methyltransferase 10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:26454]
278                                                                  pre-mRNA processing factor 18 [Source:HGNC Symbol;Acc:17351]
279                                          proteasome (prosome, macropain) 26S subunit, ATPase, 3 [Source:HGNC Symbol;Acc:9549]
280                                                        cellular retinoic acid binding protein 1 [Source:HGNC Symbol;Acc:2338]
281                                                                        zinc finger protein 606 [Source:HGNC Symbol;Acc:25879]
282                      signal transducer and activator of transcription 6, interleukin-4 induced [Source:HGNC Symbol;Acc:11368]
283                                                                   ubiquitin related modifier 1 [Source:HGNC Symbol;Acc:28378]
284                                                                       ENTH domain containing 2 [Source:HGNC Symbol;Acc:26458]
285                                                                                       myosin VB [Source:HGNC Symbol;Acc:7603]
286                                                                        zinc finger protein 226 [Source:HGNC Symbol;Acc:13019]
287                                                                  ataxia, cerebellar, Cayman type [Source:HGNC Symbol;Acc:779]
288                                                       Fas (TNFRSF6)-associated via death domain [Source:HGNC Symbol;Acc:3573]
289                                                     DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A [Source:HGNC Symbol;Acc:25628]
290                             ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 [Source:HGNC Symbol;Acc:12587]
291                                                              carnitine palmitoyltransferase 1C [Source:HGNC Symbol;Acc:18540]
292                                                                                     biotinidase [Source:HGNC Symbol;Acc:1122]
293                                                                 torsin A interacting protein 2 [Source:HGNC Symbol;Acc:24055]
294                                                          transmembrane 4 L six family member 1 [Source:HGNC Symbol;Acc:11853]
295                                                                        zinc finger protein 764 [Source:HGNC Symbol;Acc:28200]
296                                                                           galactosidase, beta 1 [Source:HGNC Symbol;Acc:4298]
297                                             nuclear transcription factor, X-box binding-like 1 [Source:HGNC Symbol;Acc:18726]
298                                                                                       KIAA0232 [Source:HGNC Symbol;Acc:28992]
299                                                                        zinc finger protein 672 [Source:HGNC Symbol;Acc:26179]
300                                               carbohydrate (chondroitin 4) sulfotransferase 11 [Source:HGNC Symbol;Acc:17422]
301                                                            regulator of G-protein signaling 19 [Source:HGNC Symbol;Acc:13735]
302                                                                   RNA methyltransferase like 1 [Source:HGNC Symbol;Acc:18485]
303 Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa [Source:HGNC Symbol;Acc:7417]
304                                                   family with sequence similarity 71, member D [Source:HGNC Symbol;Acc:20101]
305                                                     Sjogren syndrome/scleroderma autoantigen 1 [Source:HGNC Symbol;Acc:11328]
306                                                                  FK506 binding protein 2, 13kDa [Source:HGNC Symbol;Acc:3718]
307                                                                        ArfGAP with FG repeats 1 [Source:HGNC Symbol;Acc:5175]
308                         membrane-associated ring finger (C3HC4) 3, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:28728]
309                                                            chromosome 12 open reading frame 76 [Source:HGNC Symbol;Acc:33790]
310                                                                     transmembrane protein 167A [Source:HGNC Symbol;Acc:28330]
311                                                                                   MARCKS-like 1 [Source:HGNC Symbol;Acc:7142]
312            CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:HGNC Symbol;Acc:17077]
313                                                         apoptosis-inducing, TAF9-like domain 1 [Source:HGNC Symbol;Acc:23163]
314                                                                      ras homolog family member G [Source:HGNC Symbol;Acc:672]
315                                                                                    anoctamin 6 [Source:HGNC Symbol;Acc:25240]
316                                                                   ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]
317                                              adaptor-related protein complex 3, sigma 1 subunit [Source:HGNC Symbol;Acc:2013]
318                                                                 FLT3-interacting zinc finger 1 [Source:HGNC Symbol;Acc:25917]
319                                                                         dCTP pyrophosphatase 1 [Source:HGNC Symbol;Acc:28777]
320                                           proteasome (prosome, macropain) assembly chaperone 4 [Source:HGNC Symbol;Acc:21108]
321                                                                         regulatory factor X, 7 [Source:HGNC Symbol;Acc:25777]
322                                   solute carrier family 35 (GDP-fucose transporter), member C1 [Source:HGNC Symbol;Acc:20197]
323                                                    2-aminoethanethiol (cysteamine) dioxygenase [Source:HGNC Symbol;Acc:23506]
324                                                            chromosome 11 open reading frame 54 [Source:HGNC Symbol;Acc:30204]
325                                                                        zinc finger protein 320 [Source:HGNC Symbol;Acc:13842]
326                                                                           proline rich 14-like [Source:HGNC Symbol;Acc:28738]
327                                                                         transducer of ERBB2, 2 [Source:HGNC Symbol;Acc:11980]
328                                                 protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]
329                                                                         histone cluster 1, H2ak [Source:HGNC Symbol;Acc:4726]
330                                                 tumor necrosis factor, alpha-induced protein 2 [Source:HGNC Symbol;Acc:11895]
331                                                               SET and MYND domain containing 3 [Source:HGNC Symbol;Acc:15513]
332                                                                          EP400 N-terminal like [Source:HGNC Symbol;Acc:26602]
333                                                 developmentally regulated GTP binding protein 1 [Source:HGNC Symbol;Acc:3029]
334                                                    ankyrin repeat and FYVE domain containing 1 [Source:HGNC Symbol;Acc:20763]
335                                      ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 [Source:HGNC Symbol;Acc:16925]
336                                                                       breakpoint cluster region [Source:HGNC Symbol;Acc:1014]
337                                                                                 forkhead box D3 [Source:HGNC Symbol;Acc:3804]
338                                                                              metallothionein 1X [Source:HGNC Symbol;Acc:7405]
339                                                                              prothymosin, alpha [Source:HGNC Symbol;Acc:9623]
340                                                                  uroporphyrinogen III synthase [Source:HGNC Symbol;Acc:12592]
341                                                               S100 calcium binding protein A14 [Source:HGNC Symbol;Acc:18901]
342                                                                         histone cluster 1, H2bm [Source:HGNC Symbol;Acc:4750]
343                                                                       golgin A6 family-like 20 [Source:HGNC Symbol;Acc:49391]
344                                                            dynein, cytoplasmic 1, heavy chain 1 [Source:HGNC Symbol;Acc:2961]
345                                                           chromosome 20 open reading frame 112 [Source:HGNC Symbol;Acc:16106]
346                                                                         histone cluster 1, H2bh [Source:HGNC Symbol;Acc:4755]
347                                                                                       myosin IC [Source:HGNC Symbol;Acc:7597]
348                                                                      transcription factor Dp-1 [Source:HGNC Symbol;Acc:11749]
349                                                       zinc finger with KRAB and SCAN domains 8 [Source:HGNC Symbol;Acc:12983]
350                                                                         zinc finger protein 26 [Source:HGNC Symbol;Acc:13053]
351                                                                        zinc finger protein 480 [Source:HGNC Symbol;Acc:23305]
352                                 LPS-responsive vesicle trafficking, beach and anchor containing [Source:HGNC Symbol;Acc:1742]
353                                                                     COP9 signalosome subunit 8 [Source:HGNC Symbol;Acc:24335]
354                                                        structural maintenance of chromosomes 5 [Source:HGNC Symbol;Acc:20465]
355                                                            chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
356                                                        armadillo repeat containing, X-linked 6 [Source:HGNC Symbol;Acc:26094]
357                                                     long intergenic non-protein coding RNA 632 [Source:HGNC Symbol;Acc:27865]
358                                                 transcription elongation factor A (SII)-like 6 [Source:HGNC Symbol;Acc:24553]
359                                                    negative elongation factor complex member E [Source:HGNC Symbol;Acc:13974]
360                                                  family with sequence similarity 155, member A [Source:HGNC Symbol;Acc:33877]
361                                                        coiled-coil alpha-helical rod protein 1 [Source:HGNC Symbol;Acc:13930]
362                                                           mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]
363                                              succinate dehydrogenase complex assembly factor 1 [Source:HGNC Symbol;Acc:33867]
364                                                              coiled-coil domain containing 85C [Source:HGNC Symbol;Acc:35459]
365                                                        small EDRK-rich factor 1B (centromeric) [Source:HGNC Symbol;Acc:10756]
366                                                                    lin-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:19856]
367                                                     RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]
368                                                                               nucleoporin 62kDa [Source:HGNC Symbol;Acc:8066]
369                                                            hexosaminidase A (alpha polypeptide) [Source:HGNC Symbol;Acc:4878]
370                                                                        zinc finger protein 134 [Source:HGNC Symbol;Acc:12918]
371                                                                          UBX domain protein 2B [Source:HGNC Symbol;Acc:27035]
372                                                  family with sequence similarity 200, member A [Source:HGNC Symbol;Acc:25401]
373                                                                     nucleolar protein 7, 27kDa [Source:HGNC Symbol;Acc:21040]
374                                            oligosaccharyltransferase 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:32483]
375                                                    nicotinamide phosphoribosyltransferase-like [Source:HGNC Symbol;Acc:17633]
376                                                                      transmembrane protein 189 [Source:HGNC Symbol;Acc:16735]
377                                                        2,4-dienoyl CoA reductase 2, peroxisomal [Source:HGNC Symbol;Acc:2754]
378                                                     methionyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:25133]
379                                                    MPV17 mitochondrial membrane protein-like 2 [Source:HGNC Symbol;Acc:28177]
380                                                                                       KIAA0754 [Source:HGNC Symbol;Acc:29111]
381                                           polymerase (DNA directed), gamma 2, accessory subunit [Source:HGNC Symbol;Acc:9180]
382                                                             zinc finger, BED-type containing 6 [Source:HGNC Symbol;Acc:33273]
383                            sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3 [Source:HGNC Symbol;Acc:11455]
384                                                                dynein, light chain, LC8-type 2 [Source:HGNC Symbol;Acc:24596]
385                                                Spi-B transcription factor (Spi-1/PU.1 related) [Source:HGNC Symbol;Acc:11242]

Protein-protein interaction

Export significant genes.

write.table(rownames(molecules_ENSG[F.p.adj < .05, ]), 
            file = "../data/genelist-cv-sig.txt", 
            row.names = FALSE, col.names = FALSE, quote = FALSE)

Use string analysis data base to look for protein protein interaction of these differential CV genes.

This is the confidence view. Stronger associations are represented by thicker lines. This is the confidence view

This is the evidence view. Different line colors represent the types of evidence for the association. This is the evidence view

GO analysis

[Description and steps are copied from my work with Sidney]

GOstats performed Hypergeometric test for gene set enrichment. The test can take account into the conditional relationship between GO terms. Standard GOstats output contains the following information:

  1. GPID: GO term ID number
  2. Pvalue: p-vlaue of the Hypergeometric test for over-representation
  3. OddsRatio: effect size
  4. ExpCount: expected number of genes
  5. Count: observed number of genes
  6. Size: number of possible genes given the defined gene universe

GO analysis workflow is consisted of two major steps. First, we identified GO terms significant enriched given a p-value cutoff, which we set to 1 so that all possible GO terms associated with the genes can be included. We do this to eliminate false negatives. Then, we take the union of the GO terms across functional categories of interest (e.g., translation attentuation and post-translational buffering). The GO terms that are significant in at least one of the four functional categories are presented in the results.

Note. The following heatmaps are generated based on the p-values of the gene sets.

if (file.exists("rda/cv-annotation/go-cv.rda")) {
  load("rda/cv-annotation/go-cv.rda")  
} else {
go_sig_cv <- GOtest(my_ensembl_gene_universe = rownames(molecules_ENSG),
              my_ensembl_gene_test = rownames(molecules_ENSG)[F.p.adj < .05],
              pval_cutoff = 1, ontology=c("BP","CC","MF") )
save(molecules_ENSG,
     F.p.adj, go_sig_cv, file = "rda/cv-annotation/go-cv.rda")
}

Extract terms

if (file.exists("rda/cv-annotation/go-cv-terms.rda")) {
  load("rda/cv-annotation/go-cv-terms.rda")  
} else {
  # Biological process
  goterms_bp <- summary(go_sig_cv$GO$BP, pvalue = 1)
  goterms_bp <- data.frame(ID = goterms_bp[[1]],
                           Pvalue = goterms_bp[[2]],
                           Terms = goterms_bp[[7]])
  goterms_bp <- goterms_bp[order(goterms_bp$Pvalue), ]
  
  # Cellular component
  goterms_cc <- summary(go_sig_cv$GO$CC, pvalue = 1)
  goterms_cc <- data.frame(ID = goterms_cc[[1]],
                           Pvalue = goterms_cc[[2]],
                           Terms = goterms_cc[[7]])
  goterms_cc <- goterms_cc[order(goterms_cc$Pvalue), ]

  # Molecular function
  goterms_mf <- summary(go_sig_cv$GO$MF, pvalue = 1)
  goterms_mf <- data.frame(ID = goterms_mf[[1]],
                           Pvalue = goterms_mf[[2]],
                           Terms = goterms_mf[[7]])
  goterms_mf <- goterms_mf[order(goterms_mf$Pvalue), ]

  save(goterms_bp, goterms_cc, goterms_mf, 
       file = "rda/cv-annotation/go-cv-terms.rda")
}

*Biological process

dim(goterms_bp)
[1] 1899    3
kable(goterms_bp[1:50, ])
ID Pvalue Terms
GO:0071294 0.0000000 cellular response to zinc ion
GO:0010043 0.0000000 response to zinc ion
GO:0071276 0.0000000 cellular response to cadmium ion
GO:0046686 0.0000043 response to cadmium ion
GO:0071248 0.0000050 cellular response to metal ion
GO:1990267 0.0000079 response to transition metal nanoparticle
GO:0071241 0.0000120 cellular response to inorganic substance
GO:0045926 0.0000139 negative regulation of growth
GO:0010950 0.0001659 positive regulation of endopeptidase activity
GO:0010952 0.0003076 positive regulation of peptidase activity
GO:0036017 0.0004702 response to erythropoietin
GO:0036018 0.0004702 cellular response to erythropoietin
GO:0045091 0.0004702 regulation of single stranded viral RNA replication via double stranded DNA intermediate
GO:0043280 0.0007251 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0040008 0.0008488 regulation of growth
GO:2001056 0.0009056 positive regulation of cysteine-type endopeptidase activity
GO:0039692 0.0011619 single stranded viral RNA replication via double stranded DNA intermediate
GO:0071371 0.0011619 cellular response to gonadotropin stimulus
GO:0009611 0.0012159 response to wounding
GO:0045862 0.0012961 positive regulation of proteolysis
GO:0070979 0.0013827 protein K11-linked ubiquitination
GO:0052548 0.0013872 regulation of endopeptidase activity
GO:0070316 0.0016172 regulation of G0 to G1 transition
GO:0010038 0.0017304 response to metal ion
GO:0001101 0.0019230 response to acid chemical
GO:0052547 0.0019253 regulation of peptidase activity
GO:0045023 0.0021437 G0 to G1 transition
GO:0071345 0.0033358 cellular response to cytokine stimulus
GO:0034698 0.0034054 response to gonadotropin
GO:0035456 0.0034054 response to interferon-beta
GO:0039694 0.0034054 viral RNA genome replication
GO:0039703 0.0034054 RNA replication
GO:0006978 0.0041380 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
GO:0043065 0.0044896 positive regulation of apoptotic process
GO:0043068 0.0047411 positive regulation of programmed cell death
GO:0042772 0.0049369 DNA damage response, signal transduction resulting in transcription
GO:0046688 0.0049369 response to copper ion
GO:0071229 0.0054035 cellular response to acid chemical
GO:0048519 0.0056520 negative regulation of biological process
GO:0060337 0.0057822 type I interferon signaling pathway
GO:0071357 0.0057822 cellular response to type I interferon
GO:0072210 0.0058007 metanephric nephron development
GO:0010942 0.0059608 positive regulation of cell death
GO:0044707 0.0060654 single-multicellular organism process
GO:0034340 0.0061873 response to type I interferon
GO:1903900 0.0065011 regulation of viral life cycle
GO:0045069 0.0066088 regulation of viral genome replication
GO:0043281 0.0067085 regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0001975 0.0067283 response to amphetamine
GO:0040007 0.0068687 growth

*Cellular component

dim(goterms_cc)
[1] 230   3
kable(goterms_cc[1:50, ])
ID Pvalue Terms
GO:0000152 0.0029964 nuclear ubiquitin ligase complex
GO:0032797 0.0045608 SMN complex
GO:0097504 0.0045608 Gemini of coiled bodies
GO:0031519 0.0053634 PcG protein complex
GO:0019035 0.0094132 viral integration complex
GO:0035098 0.0096514 ESC/E(Z) complex
GO:0034719 0.0108718 SMN-Sm protein complex
GO:0005680 0.0149138 anaphase-promoting complex
GO:0000151 0.0177601 ubiquitin ligase complex
GO:0008043 0.0187388 intracellular ferritin complex
GO:0009330 0.0187388 DNA topoisomerase complex (ATP-hydrolyzing)
GO:0070288 0.0187388 ferritin complex
GO:0001740 0.0279776 Barr body
GO:0097440 0.0279776 apical dendrite
GO:0043204 0.0341473 perikaryon
GO:0061200 0.0371304 clathrin-sculpted gamma-aminobutyric acid transport vesicle
GO:0061202 0.0371304 clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane
GO:0072562 0.0448923 blood microparticle
GO:0000805 0.0461979 X chromosome
GO:0060198 0.0461979 clathrin-sculpted vesicle
GO:0000276 0.0551810 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
GO:0000974 0.0551810 Prp19 complex
GO:0030870 0.0551810 Mre11 complex
GO:0031461 0.0556633 cullin-RING ubiquitin ligase complex
GO:0005681 0.0571076 spliceosomal complex
GO:0035102 0.0640804 PRC1 complex
GO:0015030 0.0642553 Cajal body
GO:0048471 0.0781674 perinuclear region of cytoplasm
GO:0000790 0.0868045 nuclear chromatin
GO:0045263 0.0988565 proton-transporting ATP synthase complex, coupling factor F(o)
GO:0031011 0.1073490 Ino80 complex
GO:0033202 0.1073490 DNA helicase complex
GO:0043025 0.1100471 neuronal cell body
GO:0030018 0.1123741 Z disc
GO:0008076 0.1157623 voltage-gated potassium channel complex
GO:0005912 0.1219669 adherens junction
GO:0034705 0.1240971 potassium channel complex
GO:0035097 0.1247547 histone methyltransferase complex
GO:0070161 0.1327431 anchoring junction
GO:0031674 0.1342464 I band
GO:0000785 0.1405080 chromatin
GO:0031093 0.1486384 platelet alpha granule lumen
GO:0033177 0.1486384 proton-transporting two-sector ATPase complex, proton-transporting domain
GO:0035861 0.1486384 site of double-strand break
GO:0034774 0.1566668 secretory granule lumen
GO:0000228 0.1581837 nuclear chromosome
GO:0097346 0.1646203 INO80-type complex
GO:0044297 0.1691931 cell body
GO:1902494 0.1702408 catalytic complex
GO:0005925 0.1704578 focal adhesion

*Molecular function

dim(goterms_mf)
[1] 285   3
kable(goterms_mf[1:50, ])
ID Pvalue Terms
GO:0005520 0.0041803 insulin-like growth factor binding
GO:0004556 0.0082278 alpha-amylase activity
GO:0004595 0.0082278 pantetheine-phosphate adenylyltransferase activity
GO:0004949 0.0082278 cannabinoid receptor activity
GO:0016160 0.0082278 amylase activity
GO:0008270 0.0089991 zinc ion binding
GO:0061631 0.0093864 ubiquitin conjugating enzyme activity
GO:0061650 0.0104352 ubiquitin-like protein conjugating enzyme activity
GO:0046914 0.0112368 transition metal ion binding
GO:0008201 0.0119451 heparin binding
GO:0005178 0.0130937 integrin binding
GO:0003883 0.0163887 CTP synthase activity
GO:0004140 0.0163887 dephospho-CoA kinase activity
GO:0016900 0.0163887 oxidoreductase activity, acting on the CH-OH group of donors, disulfide as acceptor
GO:0032090 0.0163887 Pyrin domain binding
GO:0047057 0.0163887 vitamin-K-epoxide reductase (warfarin-sensitive) activity
GO:1990254 0.0163887 keratin filament binding
GO:0005539 0.0220635 glycosaminoglycan binding
GO:0004322 0.0244834 ferroxidase activity
GO:0005251 0.0244834 delayed rectifier potassium channel activity
GO:0008199 0.0244834 ferric iron binding
GO:0016724 0.0244834 oxidoreductase activity, oxidizing metal ions, oxygen as acceptor
GO:1990050 0.0244834 phosphatidic acid transporter activity
GO:0000774 0.0325124 adenyl-nucleotide exchange factor activity
GO:0003918 0.0325124 DNA topoisomerase type II (ATP-hydrolyzing) activity
GO:0005212 0.0325124 structural constituent of eye lens
GO:0061505 0.0325124 DNA topoisomerase II activity
GO:0003696 0.0404761 satellite DNA binding
GO:0008494 0.0404761 translation activator activity
GO:0055131 0.0404761 C3HC4-type RING finger domain binding
GO:0003916 0.0483751 DNA topoisomerase activity
GO:0019215 0.0483751 intermediate filament binding
GO:0030368 0.0483751 interleukin-17 receptor activity
GO:0070087 0.0483751 chromo shadow domain binding
GO:0008083 0.0485652 growth factor activity
GO:0050839 0.0540124 cell adhesion molecule binding
GO:0044877 0.0550545 macromolecular complex binding
GO:0019237 0.0562100 centromeric DNA binding
GO:1901681 0.0605070 sulfur compound binding
GO:0008144 0.0635227 drug binding
GO:0004862 0.0639812 cAMP-dependent protein kinase inhibitor activity
GO:0008139 0.0639812 nuclear localization sequence binding
GO:0042826 0.0680492 histone deacetylase binding
GO:0008301 0.0716892 DNA binding, bending
GO:0090079 0.0716892 translation regulator activity, nucleic acid binding
GO:0048038 0.0793346 quinone binding
GO:0051787 0.0793346 misfolded protein binding
GO:0061630 0.0846794 ubiquitin protein ligase activity
GO:0008656 0.0869178 cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0016722 0.0869178 oxidoreductase activity, oxidizing metal ions

Session information

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] biomaRt_2.24.1   gridExtra_2.0.0  broman_0.59-5    zoo_1.7-12      
 [5] ggplot2_1.0.1    edgeR_3.10.5     limma_3.24.15    dplyr_0.4.3     
 [9] data.table_1.9.6 knitr_1.11      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2          highr_0.5.1          GenomeInfoDb_1.4.3  
 [4] formatR_1.2.1        plyr_1.8.3           bitops_1.0-6        
 [7] tools_3.2.1          digest_0.6.8         RSQLite_1.0.0       
[10] evaluate_0.8         gtable_0.1.2         lattice_0.20-33     
[13] DBI_0.3.1            yaml_2.1.13          parallel_3.2.1      
[16] proto_0.3-10         stringr_1.0.0        IRanges_2.2.9       
[19] S4Vectors_0.6.6      stats4_3.2.1         Biobase_2.28.0      
[22] R6_2.1.1             AnnotationDbi_1.30.1 XML_3.98-1.3        
[25] rmarkdown_0.8.1      reshape2_1.4.1       magrittr_1.5        
[28] BiocGenerics_0.14.0  scales_0.3.0         htmltools_0.2.6     
[31] MASS_7.3-45          assertthat_0.1       colorspace_1.2-6    
[34] labeling_0.3         stringi_1.0-1        RCurl_1.95-4.7      
[37] munsell_0.4.2        chron_2.3-47