LDL - Expression and Splicing Jointly
Sheng Qian
2022-12-17
Last updated: 2023-02-03
Checks: 5 2
Knit directory: cTWAS_analysis/
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| absolute | relative |
|---|---|
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/ | data |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config_b38.R | code/ctwas_config_b38.R |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mashr_sqtl/sqtl/mashr/mashr_Liver_Splicing_mapping.RData | data/mashr_sqtl/sqtl/mashr/mashr_Liver_Splicing_mapping.RData |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mashr_sqtl/sqtl/mashr/mashr_Whole_Blood_Splicing_mapping.RData | data/mashr_sqtl/sqtl/mashr/mashr_Whole_Blood_Splicing_mapping.RData |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mqtl/WholeBlood.db | data/mqtl/WholeBlood.db |
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analysis_id <- params$analysis_id
trait_id <- params$trait_id
weight <- params$weight
results_dir <- paste0("/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/", trait_id, "/", weight)
source("/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config_b38.R")
options(digits = 4)Load ctwas results
Check convergence of parameters
#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior) SNP Whole_Blood Whole_Blood_Splicing
0.0001751 0.0225055 0.0052580
Whole_Blood_Methylation
0.0108737 #estimated group prior variance
estimated_group_prior_var <- estimated_group_prior_var_all[,ncol(group_prior_var_rec)]
print(estimated_group_prior_var) SNP Whole_Blood Whole_Blood_Splicing
15.55 19.40 29.53
Whole_Blood_Methylation
14.35 #estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)[1] 61.79#report sample size
print(sample_size)[1] 350470#report group size
print(group_size) SNP Whole_Blood Whole_Blood_Splicing
8696600 11198 20134
Whole_Blood_Methylation
11858 #estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve) SNP Whole_Blood Whole_Blood_Splicing
0.067547 0.013950 0.008919
Whole_Blood_Methylation
0.005278 #total PVE
sum(estimated_group_pve)[1] 0.09569#attributable PVE
estimated_group_pve/sum(estimated_group_pve) SNP Whole_Blood Whole_Blood_Splicing
0.70586 0.14578 0.09320
Whole_Blood_Methylation
0.05515 #load information for all genes
sqlite <- RSQLite::dbDriver("SQLite")
db = RSQLite::dbConnect(sqlite, "/project2/compbio/predictdb/mashr_models/mashr_Whole_Blood.db")
query <- function(...) RSQLite::dbGetQuery(db, ...)
gene_info <- query("select gene, genename from extra")
RSQLite::dbDisconnect(db)
ctwas_gene_E_res$genename <- gene_info[sapply(ctwas_gene_E_res$gene_id, match, gene_info$gene),"genename"]
load("/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mashr_sqtl/sqtl/mashr/mashr_Whole_Blood_Splicing_mapping.RData")
ctwas_gene_S_res$genename <- intron_info[sapply(ctwas_gene_S_res$gene_id, match, intron_info$gene), "genename"]
sqlite <- RSQLite::dbDriver("SQLite")
db = RSQLite::dbConnect(sqlite, "/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mqtl/WholeBlood.db")
query <- function(...) RSQLite::dbGetQuery(db, ...)
gene_info <- query("select gene, genename from extra")
RSQLite::dbDisconnect(db)
ctwas_gene_M_res$genename <- gene_info[sapply(ctwas_gene_M_res$gene_id, match, gene_info$gene),"genename"]
ctwas_gene_M_res$genename <- sapply(ctwas_gene_M_res$genename, function(x){unlist(strsplit(x, split="[;]"))[1]})Top expression/intron/CpG
genename gene_id susie_pip group
39936 FES ENSG00000182511.11 1.0000 Expression
43125 YBEY intron_21_46287123_46296162 1.0000 Splicing
38047 TAGAP ENSG00000164691.16 1.0000 Expression
36651 ARHGAP15 ENSG00000075884.13 1.0000 Expression
41903 CNN2 intron_19_1032696_1036130 1.0000 Splicing
36665 BAZ2B ENSG00000123636.17 0.9999 Expression
38535 VLDLR ENSG00000147852.15 0.9999 Expression
39701 KIAA0391 ENSG00000100890.15 0.9997 Expression
38156 CREB5 ENSG00000146592.16 0.9991 Expression
37171 MED12L ENSG00000144893.12 0.9981 Expression
35946 LAPTM5 ENSG00000162511.7 0.9981 Expression
37527 SLC22A4 ENSG00000197208.5 0.9966 Expression
37106 ATXN7 ENSG00000163635.17 0.9965 Expression
39549 FLT3 intron_13_28024943_28027088 0.9949 Splicing
36279 CNIH4 ENSG00000143771.11 0.9948 Expression
39447 ALDH2 ENSG00000111275.12 0.9941 Expression
39604 LAMP1 ENSG00000185896.10 0.9931 Expression
36089 SLC25A24 ENSG00000085491.15 0.9924 Expression
43166 HDHD5 ENSG00000069998.12 0.9912 Expression
41827 TTC39C ENSG00000168234.12 0.9872 Expression
41159 YPEL2 ENSG00000175155.8 0.9846 Expression
38704 LIPA ENSG00000107798.17 0.9839 Expression
41100 KIF18B ENSG00000186185.13 0.9837 Expression
39339 ACVRL1 cg21236262 0.9824 Methylation
38973 PTPRJ ENSG00000149177.12 0.9824 Expression
37291 ARAP2 ENSG00000047365.11 0.9783 Expression
37629 CPEB4 ENSG00000113742.12 0.9741 Expression
40700 MYO1C cg02622416 0.9736 Methylation
40445 ZFPM1 ENSG00000179588.8 0.9711 Expression
38575 OSTF1 ENSG00000134996.11 0.9691 Expression
39588 KLF12 ENSG00000118922.17 0.9685 Expression
36440 ITSN2 intron_2_24209221_24209818 0.9663 Splicing
37693 ATXN1 ENSG00000124788.17 0.9616 Expression
38633 NEK6 ENSG00000119408.16 0.9567 Expression
36934 UQCRC1 ENSG00000010256.10 0.9555 Expression
40367 GLG1 ENSG00000090863.11 0.9553 Expression
37233 ADD1 ENSG00000087274.16 0.9550 Expression
37348 TET2 ENSG00000168769.13 0.9535 Expression
36222 SELL ENSG00000188404.8 0.9505 Expression
36005 CITED4 ENSG00000179862.6 0.9505 Expression
37276 TBC1D14 ENSG00000132405.18 0.9442 Expression
37664 CANX intron_5_179699102_179705679 0.9434 Splicing
36622 HS6ST1 ENSG00000136720.6 0.9385 Expression
36670 CD302 ENSG00000241399.6 0.9303 Expression
39154 CD6 cg27098804 0.9266 Methylation
36067 CDC14A ENSG00000079335.18 0.9259 Expression
37398 DDX60L ENSG00000181381.13 0.9238 Expression
42503 ATP13A1 ENSG00000105726.16 0.9228 Expression
42083 CTC-503J8.4 cg14319541 0.9227 Methylation
42362 MYO9B ENSG00000099331.13 0.9165 Expression
40361 ITGAL cg24033122 0.9158 Methylation
42233 AP1M2 ENSG00000129354.11 0.9144 Expression
39185 AP000908.1 cg04049253 0.9088 Methylation
36881 CCR8 ENSG00000179934.6 0.9073 Expression
37134 PAQR9 ENSG00000188582.8 0.9002 Expression
37511 TNFAIP8 ENSG00000145779.7 0.8984 Expression
37102 CTD-2330K9.3 cg24308560 0.8970 Methylation
37439 RAI14 ENSG00000039560.13 0.8925 Expression
38269 CPSF4 ENSG00000160917.14 0.8870 Expression
37608 ADAM19 ENSG00000135074.15 0.8862 Expression
38449 RNF139-AS1 ENSG00000245149.3 0.8838 Expression
36265 NCF2 intron_1_183570839_183573185 0.8821 Splicing
41207 SLC9A3R1 ENSG00000109062.11 0.8776 Expression
38476 RP11-136O12.2 cg09660151 0.8753 Methylation
37185 ABCC5 ENSG00000114770.16 0.8707 Expression
41423 UBE2O ENSG00000175931.12 0.8706 Expression
37312 REST ENSG00000084093.16 0.8678 Expression
39271 CERS5 intron_12_50134068_50134546 0.8677 Splicing
42844 UBOX5 ENSG00000185019.16 0.8644 Expression
36462 DTNB ENSG00000138101.18 0.8556 Expression
37475 ZBED3 ENSG00000132846.5 0.8554 Expression
39884 MEG3 ENSG00000214548.14 0.8479 Expression
38383 ACHE ENSG00000087085.13 0.8461 Expression
38011 L3MBTL3 ENSG00000198945.7 0.8426 Expression
37418 NPR3 ENSG00000113389.15 0.8420 Expression
37369 LRBA intron_4_150278004_150282450 0.8388 Splicing
37420 MTMR12 ENSG00000150712.10 0.8381 Expression
36185 RCSD1 ENSG00000198771.10 0.8329 Expression
41409 JMJD6 ENSG00000070495.14 0.8306 Expression
37118 PXYLP1 ENSG00000155893.12 0.8284 Expression
39582 KLF5 ENSG00000102554.13 0.8242 Expression
41886 ELANE ENSG00000197561.6 0.8125 Expression
38127 JAZF1 ENSG00000153814.11 0.8109 Expression
37994 HSF2 ENSG00000025156.12 0.8108 Expression
39810 ZFP36L1 ENSG00000185650.9 0.8106 Expression
42600 LSM4 cg15796753 0.8058 Methylation
38758 RBP4 ENSG00000138207.13 0.8035 ExpressionTop genes by expression/splicing/methylation
ctwas_gene_E_res <- ctwas_gene_res[ctwas_gene_res$group=="Expression",]
ctwas_gene_S_res <- ctwas_gene_res[ctwas_gene_res$group=="Splicing",]
ctwas_gene_M_res <- ctwas_gene_res[ctwas_gene_res$group=="Methylation",]
df_gene_E <- aggregate(ctwas_gene_E_res$susie_pip,by=list(ctwas_gene_E_res$genename), FUN=sum)
colnames(df_gene_E) <- c("genename", "susie_pip")
df_gene_E$group <- "Expression"
df_gene_S <- aggregate(ctwas_gene_S_res$susie_pip,by=list(ctwas_gene_S_res$genename), FUN=sum)
colnames(df_gene_S) <- c("genename", "susie_pip")
df_gene_S$group <- "Splicing"
df_gene_M <- aggregate(ctwas_gene_M_res$susie_pip,by=list(ctwas_gene_M_res$genename), FUN=sum)
colnames(df_gene_M) <- c("genename", "susie_pip")
df_gene_M$group <- "Methylation"
df_gene <- rbind(df_gene_E,df_gene_S,df_gene_M)
head(df_gene[order(-df_gene$susie_pip),], max(sum(df_gene$susie_pip>0.8), 20)) genename susie_pip group
14585 MYO1G 1.3514 Splicing
21011 NINJ2 1.1701 Methylation
17145 TSPAN32 1.1599 Splicing
18178 AMZ1 1.0639 Methylation
13814 ITSN2 1.0254 Splicing
16153 SIRPB1 1.0210 Splicing
21542 PTPRN2 1.0060 Methylation
14179 LYZ 1.0001 Splicing
12347 CNN2 1.0000 Splicing
3340 FES 1.0000 Expression
17524 YBEY 1.0000 Splicing
9381 TAGAP 1.0000 Expression
612 ARHGAP15 1.0000 Expression
906 BAZ2B 0.9999 Expression
10464 VLDLR 0.9999 Expression
4601 KIAA0391 0.9997 Expression
15547 RAB34 0.9995 Splicing
2141 CREB5 0.9991 Expression
19483 ELK3 0.9989 Methylation
5430 MED12L 0.9981 Expression
4787 LAPTM5 0.9981 Expression
15509 PVT1 0.9970 Splicing
8729 SLC22A4 0.9966 Expression
842 ATXN7 0.9965 Expression
13190 FLT3 0.9955 Splicing
1966 CNIH4 0.9948 Expression
379 ALDH2 0.9941 Expression
11991 CANX 0.9939 Splicing
4777 LAMP1 0.9931 Expression
8746 SLC25A24 0.9924 Expression
3989 HDHD5 0.9912 Expression
22612 SPTLC2 0.9895 Methylation
10159 TTC39C 0.9872 Expression
10660 YPEL2 0.9846 Expression
5067 LIPA 0.9839 Expression
4637 KIF18B 0.9837 Expression
18048 ACVRL1 0.9824 Methylation
7334 PTPRJ 0.9824 Expression
16974 TNFRSF1A 0.9794 Splicing
593 ARAP2 0.9783 Expression
2102 CPEB4 0.9741 Expression
20919 MYO1C 0.9736 Methylation
10770 ZFPM1 0.9711 Expression
22247 RRBP1 0.9698 Methylation
6450 OSTF1 0.9691 Expression
4669 KLF12 0.9685 Expression
836 ATXN1 0.9616 Expression
6067 NEK6 0.9567 Expression
10365 UQCRC1 0.9555 Expression
3654 GLG1 0.9553 Expression
236 ADD1 0.9550 Expression
9518 TET2 0.9535 Expression
22284 SBNO2 0.9509 Methylation
8491 SELL 0.9505 Expression
1860 CITED4 0.9505 Expression
20541 LINC01344 0.9445 Methylation
9417 TBC1D14 0.9442 Expression
14644 NCF2 0.9422 Splicing
4174 HS6ST1 0.9385 Expression
16859 TMCC2 0.9337 Splicing
1581 CD302 0.9303 Expression
18771 CD6 0.9266 Methylation
1618 CDC14A 0.9259 Expression
2499 DDX60L 0.9238 Expression
784 ATP13A1 0.9228 Expression
19114 CTC-503J8.4 0.9227 Methylation
5891 MYO9B 0.9165 Expression
20201 ITGAL 0.9161 Methylation
526 AP1M2 0.9144 Expression
18232 AP000908.1 0.9088 Methylation
1540 CCR8 0.9073 Expression
14342 MFSD13A 0.9073 Splicing
15435 PSD4 0.9016 Splicing
6532 PAQR9 0.9002 Expression
9851 TNFAIP8 0.8984 Expression
19159 CTD-2330K9.3 0.8970 Methylation
23167 ZBTB2 0.8967 Methylation
7466 RAI14 0.8925 Expression
2118 CPSF4 0.8870 Expression
209 ADAM19 0.8862 Expression
17450 WDFY2 0.8849 Splicing
7727 RNF139-AS1 0.8838 Expression
8873 SLC9A3R1 0.8776 Expression
21805 RP11-136O12.2 0.8753 Methylation
38 ABCC5 0.8707 Expression
10268 UBE2O 0.8706 Expression
7605 REST 0.8678 Expression
12228 CERS5 0.8677 Splicing
10288 UBOX5 0.8644 Expression
15191 PLCB2 0.8623 Splicing
19656 FBRSL1 0.8596 Methylation
2724 DTNB 0.8556 Expression
10678 ZBED3 0.8554 Expression
5455 MEG3 0.8479 Expression
145 ACHE 0.8461 Expression
4760 L3MBTL3 0.8426 Expression
6227 NPR3 0.8420 Expression
23028 UBE2I 0.8420 Methylation
14111 LRBA 0.8388 Splicing
5805 MTMR12 0.8381 Expression
7579 RCSD1 0.8329 Expression
4502 JMJD6 0.8306 Expression
7364 PXYLP1 0.8284 Expression
4673 KLF5 0.8242 Expression
12044 CCDC125 0.8207 Splicing
19896 GPR126 0.8181 Methylation
2884 ELANE 0.8125 Expression
4499 JAZF1 0.8109 Expression
4191 HSF2 0.8108 Expression
10760 ZFP36L1 0.8106 Expression
20619 LSM4 0.8058 Methylation
18274 APOLD1 0.8042 Methylation
7557 RBP4 0.8035 ExpressionTop genes by combined PIP
genename combined_pip expression_pip splicing_pip methylation_pip
14632 YPEL2 1.7531 0.985 0.000 0.768
6635 LAPTM5 1.7444 0.998 0.002 0.744
1036 ARHGAP15 1.7228 1.000 0.680 0.042
8086 MYO1G 1.4333 0.082 1.351 0.000
12304 SLC45A4 1.3131 0.786 0.509 0.018
3603 DDX60L 1.2453 0.924 0.322 0.000
13604 TNFAIP8 1.2375 0.898 0.120 0.219
5556 HDHD5 1.2168 0.991 0.226 0.000
8382 NINJ2 1.2094 0.033 0.006 1.170
7276 LYZ 1.1825 0.182 1.000 0.000
12684 SPTLC2 1.1762 0.187 0.000 0.989
13938 TSPAN32 1.1634 0.004 1.160 0.000
11576 RRBP1 1.1285 0.066 0.093 0.970
12119 SLC12A7 1.0927 0.416 0.011 0.666
1319 ATXN1 1.0859 0.962 0.058 0.067
383 ACAP1 1.0827 0.349 0.015 0.719
6369 KIAA0391 1.0714 1.000 0.072 0.000
6195 ITSN2 1.0710 0.033 1.025 0.013
773 AMZ1 1.0639 0.000 0.000 1.064
12080 SIRPB1 1.0583 0.037 1.021 0.000
6108 IQGAP2 1.0558 0.443 0.589 0.024
518 ADD1 1.0546 0.955 0.100 0.000
9680 PPP5C 1.0500 0.436 0.004 0.610
14724 ZDHHC18 1.0485 0.009 0.590 0.450
8411 NLRC5 1.0472 0.676 0.074 0.297
4214 EOMES 1.0430 0.645 0.009 0.389
4131 ELK3 1.0411 0.031 0.012 0.999
1325 ATXN7 1.0395 0.997 0.043 0.000
4614 FBRSL1 1.0389 0.063 0.117 0.860
13618 TNFRSF1A 1.0375 0.016 0.979 0.042
9965 PTPRJ 1.0347 0.982 0.015 0.038
13069 TBC1D14 1.0311 0.944 0.062 0.025
2270 CD101 1.0281 0.702 0.006 0.320
2797 CNIH4 1.0177 0.995 0.023 0.000
7508 MED12L 1.0147 0.998 0.000 0.017
700 ALDH2 1.0137 0.994 0.020 0.000
4709 FES 1.0119 1.000 0.012 0.000
6467 KLF12 1.0068 0.968 0.038 0.000
9969 PTPRN2 1.0060 0.000 0.000 1.006
4281 ERICH1 1.0036 0.046 0.203 0.754
14370 VLDLR 1.0036 1.000 0.004 0.000
3021 CREB5 1.0014 0.999 0.002 0.000
5641 HIST1H2BD 1.0009 0.675 0.326 0.000
13024 TAGAP 1.0007 1.000 0.001 0.000
10073 RAB34 1.0006 0.001 1.000 0.000
1413 BAZ2B 1.0005 1.000 0.001 0.000
2800 CNN2 1.0001 0.000 1.000 0.000
14611 YBEY 1.0000 0.000 1.000 0.000
8082 MYO1C 0.9998 0.026 0.000 0.974
2973 CPEB4 0.9996 0.974 0.000 0.025
1010 ARAP2 0.9992 0.978 0.021 0.000
12164 SLC22A4 0.9982 0.997 0.002 0.000
9992 PVT1 0.9970 0.000 0.997 0.000
12185 SLC25A24 0.9967 0.992 0.004 0.000
4794 FLT3 0.9955 0.000 0.995 0.000
1989 CANX 0.9939 0.000 0.994 0.000
6622 LAMP1 0.9931 0.993 0.000 0.000
8827 OSTF1 0.9924 0.969 0.023 0.000
10577 RORC 0.9913 0.776 0.000 0.216
7047 LIPA 0.9908 0.984 0.006 0.001
2305 CD33 0.9902 0.039 0.767 0.184
13990 TTC39C 0.9878 0.987 0.001 0.000
9368 PLCB2 0.9837 0.121 0.862 0.000
6422 KIF18B 0.9837 0.984 0.000 0.000
461 ACVRL1 0.9824 0.000 0.000 0.982
13753 TRAF3IP3 0.9776 0.686 0.292 0.000
13372 TMCC2 0.9776 0.044 0.934 0.000
14766 ZFPM1 0.9726 0.971 0.001 0.000
14122 UBE2I 0.9675 0.067 0.059 0.842
8311 NEK6 0.9663 0.957 0.004 0.006
8667 NUP88 0.9649 0.172 0.767 0.026
3917 DTNB 0.9621 0.856 0.005 0.102
5125 GLG1 0.9580 0.955 0.003 0.000
12320 SLC5A11 0.9579 0.302 0.000 0.656
14154 UBOX5 0.9568 0.864 0.092 0.000
13190 TET2 0.9561 0.953 0.003 0.000
14245 UQCRC1 0.9555 0.956 0.000 0.000
11857 SELL 0.9551 0.951 0.005 0.000
5796 HS6ST1 0.9546 0.939 0.000 0.016
11724 SBNO2 0.9517 0.000 0.001 0.951
2665 CITED4 0.9505 0.951 0.000 0.000
7741 MLX 0.9491 0.735 0.214 0.000
6957 LINC01344 0.9445 0.000 0.000 0.944
8211 NCF2 0.9422 0.000 0.942 0.000
14663 ZBTB2 0.9364 0.040 0.000 0.897
5386 GSAP 0.9319 0.630 0.262 0.040
2303 CD302 0.9303 0.930 0.000 0.000
2324 CD6 0.9275 0.000 0.001 0.927
2345 CDC14A 0.9259 0.926 0.000 0.000
1244 ATP13A1 0.9248 0.923 0.002 0.000
3188 CTC-503J8.4 0.9227 0.000 0.000 0.923
1782 C20orf96 0.9196 0.721 0.060 0.138
14462 WDFY2 0.9185 0.000 0.885 0.034
54 ABCC5 0.9167 0.871 0.019 0.027
8095 MYO9B 0.9166 0.917 0.000 0.000
6163 ITGAL 0.9161 0.000 0.000 0.916
928 AP1M2 0.9144 0.914 0.000 0.000
6360 KIAA0040 0.9139 0.067 0.085 0.762
10132 RAI14 0.9131 0.892 0.000 0.021
897 AP000908.1 0.9088 0.000 0.000 0.909
2253 CCR8 0.9073 0.907 0.000 0.000
7609 MFSD13A 0.9073 0.000 0.907 0.000
7989 MTMR12 0.9019 0.838 0.064 0.000
9846 PSD4 0.9016 0.000 0.902 0.000
8937 PAQR9 0.9002 0.900 0.000 0.000
472 ADAM19 0.8995 0.886 0.005 0.008
3263 CTD-2330K9.3 0.8970 0.000 0.000 0.897
11679 SAE1 0.8945 0.622 0.272 0.000
2992 CPSF4 0.8870 0.887 0.000 0.000
10482 RNF139-AS1 0.8838 0.884 0.000 0.000
7346 MAP2K5 0.8800 0.070 0.030 0.780
12350 SLC9A3R1 0.8776 0.878 0.000 0.000
2306 CD36 0.8767 0.563 0.314 0.000
10674 RP11-136O12.2 0.8753 0.000 0.000 0.875
6217 JAZF1 0.8744 0.811 0.063 0.000
7158 LRRC25 0.8725 0.735 0.137 0.000
14129 UBE2O 0.8711 0.871 0.001 0.000
8626 NUDT14 0.8711 0.216 0.557 0.098
6596 L3MBTL3 0.8697 0.843 0.000 0.027
2526 CERS5 0.8680 0.000 0.868 0.000
10311 REST 0.8678 0.868 0.000 0.000
7125 LRBA 0.8612 0.000 0.839 0.022
2194 CCDC9 0.8583 0.667 0.191 0.000
3811 DNASE1 0.8580 0.551 0.007 0.300
14655 ZBED3 0.8554 0.855 0.000 0.000
2101 CCDC125 0.8550 0.034 0.821 0.000
399 ACHE 0.8510 0.846 0.005 0.000
9934 PTK2B 0.8493 0.739 0.053 0.057
7537 MEG3 0.8479 0.848 0.000 0.000
10281 RCSD1 0.8459 0.833 0.008 0.005
9839 PRUNE2 0.8427 0.799 0.006 0.038
8514 NPR3 0.8420 0.842 0.000 0.000
6222 JMJD6 0.8357 0.831 0.005 0.000
10007 PXYLP1 0.8357 0.828 0.007 0.000
1132 ARRB2 0.8356 0.281 0.554 0.000
4136 ELMO1 0.8347 0.702 0.046 0.086
991 APOLD1 0.8331 0.029 0.000 0.804
6472 KLF5 0.8242 0.824 0.000 0.000
5285 GPR126 0.8181 0.000 0.000 0.818
7213 LSM4 0.8177 0.011 0.001 0.806
2054 CATSPER2 0.8145 0.792 0.000 0.023
4123 ELANE 0.8130 0.813 0.000 0.000
11608 RSU1 0.8115 0.037 0.270 0.505
5816 HSF2 0.8108 0.811 0.000 0.000
14754 ZFP36L1 0.8106 0.811 0.000 0.000
1045 ARHGAP26 0.8096 0.000 0.022 0.788
1065 ARHGEF12 0.8087 0.762 0.046 0.000
7412 MARK3 0.8072 0.696 0.109 0.002
15001 ZNF516 0.8067 0.792 0.004 0.011
468 ADAM10 0.8067 0.798 0.009 0.000
10256 RBP4 0.8035 0.804 0.000 0.000
13327 TLDC1 0.8018 0.079 0.000 0.723GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 152Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
Term Overlap
1 neutrophil activation involved in immune response (GO:0002283) 15/485
2 amyloid precursor protein metabolic process (GO:0042982) 4/18
3 neutrophil degranulation (GO:0043312) 14/481
4 neutrophil mediated immunity (GO:0002446) 14/488
5 adipose tissue development (GO:0060612) 3/12
Adjusted.P.value
1 0.005830
2 0.005830
3 0.007156
4 0.007156
5 0.023247
Genes
1 PTPRN2;ADAM10;PTPRJ;IQGAP2;LYZ;ITGAL;SIRPB1;CNN2;LAMP1;SELL;OSTF1;CD36;DNASE1;ELANE;CD33
2 ADAM19;ACHE;ADAM10;TMCC2
3 PTPRN2;ADAM10;PTPRJ;IQGAP2;LYZ;ITGAL;SIRPB1;CNN2;LAMP1;SELL;OSTF1;CD36;ELANE;CD33
4 PTPRN2;ADAM10;PTPRJ;IQGAP2;LYZ;ITGAL;SIRPB1;CNN2;LAMP1;SELL;OSTF1;CD36;ELANE;CD33
5 SPTLC2;ZNF516;RORC
[1] "GO_Cellular_Component_2021"
Term Overlap Adjusted.P.value
1 specific granule (GO:0042581) 8/160 0.002908
2 secretory granule membrane (GO:0030667) 10/274 0.002908
3 actin-based cell projection (GO:0098858) 5/83 0.017256
4 specific granule membrane (GO:0035579) 5/91 0.019746
5 tertiary granule (GO:0070820) 6/164 0.038873
Genes
1 CNN2;ADAM10;PTPRJ;CD36;LYZ;ITGAL;ELANE;CD33
2 PTPRN2;LAMP1;SELL;ADAM10;PTPRJ;CD36;IQGAP2;ITGAL;SIRPB1;CD33
3 SLC9A3R1;MYO1C;CD302;IQGAP2;MYO1G
4 ADAM10;PTPRJ;CD36;ITGAL;CD33
5 CNN2;PTPRN2;LAMP1;ADAM10;LYZ;CD33
[1] "GO_Molecular_Function_2021"
[1] Term Overlap Adjusted.P.value Genes
<0 rows> (or 0-length row.names)DisGeNET enrichment analysis for genes with PIP>0.5
Description FDR Ratio BgRatio
14 Refractory anaemia with excess blasts 0.09637 1/85 1/9703
45 Cholesterol Ester Storage Disease 0.09637 1/85 1/9703
71 Epistaxis 0.09637 1/85 1/9703
77 Freckles 0.09637 1/85 1/9703
109 Acute Promyelocytic Leukemia 0.09637 3/85 46/9703
112 Liver Cirrhosis, Experimental 0.09637 15/85 774/9703
122 Melanosis 0.09637 1/85 1/9703
123 Chloasma 0.09637 1/85 1/9703
176 Telangiectasis 0.09637 1/85 1/9703
187 Wolman Disease 0.09637 1/85 1/9703WebGestalt enrichment analysis for genes with PIP>0.5
Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...Warning in oraEnrichment(interestGeneList, referenceGeneList, geneSet, minNum =
minNum, : No significant gene set is identified based on FDR 0.05!NULL
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.1 cowplot_1.1.1
[5] ggplot2_3.4.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] httr_1.4.4 sass_0.4.4 bit64_4.0.5 vroom_1.6.0
[5] jsonlite_1.8.4 foreach_1.5.2 bslib_0.4.1 assertthat_0.2.1
[9] getPass_0.2-2 highr_0.9 doRNG_1.8.2 yaml_2.3.6
[13] pillar_1.8.1 lattice_0.20-44 glue_1.6.2 digest_0.6.31
[17] promises_1.2.0.1 colorspace_2.0-3 htmltools_0.5.4 httpuv_1.6.7
[21] Matrix_1.3-3 plyr_1.8.8 pkgconfig_2.0.3 scales_1.2.1
[25] processx_3.8.0 svglite_2.1.0 whisker_0.4.1 later_1.3.0
[29] tzdb_0.3.0 git2r_0.30.1 tibble_3.1.8 generics_0.1.3
[33] farver_2.1.0 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
[37] cli_3.4.1 crayon_1.5.2 magrittr_2.0.3 evaluate_0.19
[41] ps_1.7.2 apcluster_1.4.10 fs_1.5.2 fansi_1.0.3
[45] doParallel_1.0.17 tools_4.1.0 data.table_1.14.6 hms_1.1.2
[49] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 rngtools_1.5.2
[53] callr_3.7.3 compiler_4.1.0 jquerylib_0.1.4 systemfonts_1.0.4
[57] rlang_1.0.6 grid_4.1.0 iterators_1.0.14 rstudioapi_0.14
[61] rjson_0.2.21 igraph_1.3.5 labeling_0.4.2 rmarkdown_2.19
[65] gtable_0.3.1 codetools_0.2-18 DBI_1.1.3 curl_4.3.2
[69] reshape2_1.4.4 R6_2.5.1 knitr_1.41 dplyr_1.0.10
[73] bit_4.0.5 fastmap_1.1.0 utf8_1.2.2 rprojroot_2.0.3
[77] readr_2.1.3 stringi_1.7.8 parallel_4.1.0 Rcpp_1.0.9
[81] vctrs_0.5.1 tidyselect_1.2.0 xfun_0.35