Last updated: 2023-02-02

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Knit directory: cTWAS_analysis/

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/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
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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

Version Author Date
a762568 sq-96 2023-02-02
c5aaf96 sq-96 2023-02-02
#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  Expression

Top 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  Expression

Top 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           0.723

GO enrichment analysis for genes with PIP>0.5

#number of genes for gene set enrichment
length(genes)
[1] 47
Uploading 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"

[1] Term             Overlap          Adjusted.P.value Genes           
<0 rows> (or 0-length row.names)
[1] "GO_Cellular_Component_2021"

[1] Term             Overlap          Adjusted.P.value Genes           
<0 rows> (or 0-length row.names)
[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
1           Abortion, Habitual 0.04948  1/28   2/9703
10         Atrial Fibrillation 0.04948  3/28 160/9703
37      Dysautonomia, Familial 0.04948  1/28   3/9703
41                    Freckles 0.04948  1/28   1/9703
53                   Melanosis 0.04948  1/28   1/9703
54                    Chloasma 0.04948  1/28   1/9703
68            Reflex, Abnormal 0.04948  1/28   5/9703
83     Ataxia, Spinocerebellar 0.04948  2/28  34/9703
85 Intermittent joint effusion 0.04948  1/28   2/9703
86  Reflex, Corneal, Decreased 0.04948  1/28   5/9703

WebGestalt 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