Atrial fibrillation - Heart Atrial Appendage
sheng Qian
2021-12-18
Last updated: 2021-12-22
Checks: 6 1
Knit directory: cTWAS_analysis/
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Load ctwas results
Gene set enrichment for genes with PIP>0.8
#GO enrichment analysis
library(enrichR)Welcome to enrichR
Checking connection ... Enrichr ... Connection is Live!
FlyEnrichr ... Connection is available!
WormEnrichr ... Connection is available!
YeastEnrichr ... Connection is available!
FishEnrichr ... Connection is available!dbs <- c("GO_Biological_Process_2021", "GO_Cellular_Component_2021", "GO_Molecular_Function_2021")
genes <- ctwas_gene_res$genename[ctwas_gene_res$susie_pip>0.8]
#number of genes for gene set enrichment
length(genes)[1] 32if (length(genes)>0){
GO_enrichment <- enrichr(genes, dbs)
for (db in dbs){
print(db)
df <- GO_enrichment[[db]]
print(plotEnrich(GO_enrichment[[db]]))
df <- df[df$Adjusted.P.value<0.05,c("Term", "Overlap", "Adjusted.P.value", "Genes")]
print(df)
}
#DisGeNET enrichment
# devtools::install_bitbucket("ibi_group/disgenet2r")
library(disgenet2r)
disgenet_api_key <- get_disgenet_api_key(
email = "wesleycrouse@gmail.com",
password = "uchicago1" )
Sys.setenv(DISGENET_API_KEY= disgenet_api_key)
res_enrich <-disease_enrichment(entities=genes, vocabulary = "HGNC",
database = "CURATED" )
df <- res_enrich@qresult[1:10, c("Description", "FDR", "Ratio", "BgRatio")]
print(df)
#WebGestalt enrichment
library(WebGestaltR)
background <- ctwas_gene_res$genename
#listGeneSet()
databases <- c("pathway_KEGG", "disease_GLAD4U", "disease_OMIM")
enrichResult <- WebGestaltR(enrichMethod="ORA", organism="hsapiens",
interestGene=genes, referenceGene=background,
enrichDatabase=databases, interestGeneType="genesymbol",
referenceGeneType="genesymbol", isOutput=F)
print(enrichResult[,c("description", "size", "overlap", "FDR", "database", "userId")])
}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)AES gene(s) from the input list not found in DisGeNET CURATEDBOK gene(s) from the input list not found in DisGeNET CURATEDCMTM5 gene(s) from the input list not found in DisGeNET CURATEDJAM2 gene(s) from the input list not found in DisGeNET CURATEDRP11-325L7.2 gene(s) from the input list not found in DisGeNET CURATEDSTK11IP gene(s) from the input list not found in DisGeNET CURATEDLINC01629 gene(s) from the input list not found in DisGeNET CURATEDSP100 gene(s) from the input list not found in DisGeNET CURATEDDLEU1 gene(s) from the input list not found in DisGeNET CURATEDMURC gene(s) from the input list not found in DisGeNET CURATEDPOPDC3 gene(s) from the input list not found in DisGeNET CURATEDSEC23IP gene(s) from the input list not found in DisGeNET CURATEDAGAP5 gene(s) from the input list not found in DisGeNET CURATEDMARS gene(s) from the input list not found in DisGeNET CURATEDRP5-890E16.5 gene(s) from the input list not found in DisGeNET CURATED Description
5 Atrial Fibrillation
85 Paroxysmal atrial fibrillation
156 Persistent atrial fibrillation
171 familial atrial fibrillation
37 Cardiomegaly
130 Cardiac Hypertrophy
58 Congenital retrognathism
157 HYPOTHYROIDISM, CONGENITAL, NONGOITROUS, 5 (disorder)
158 Lipodystrophy, Congenital Generalized, Type 3
167 ATRIAL SEPTAL DEFECT 7 WITH OR WITHOUT ATRIOVENTRICULAR CONDUCTION DEFECTS
FDR Ratio BgRatio
5 7.915974e-11 9/17 160/9703
85 7.915974e-11 9/17 156/9703
156 7.915974e-11 9/17 156/9703
171 7.915974e-11 9/17 156/9703
37 1.217805e-02 3/17 82/9703
130 1.217805e-02 3/17 82/9703
58 1.467481e-02 1/17 1/9703
157 1.467481e-02 1/17 1/9703
158 1.467481e-02 1/17 1/9703
167 1.467481e-02 1/17 1/9703******************************************
* *
* Welcome to WebGestaltR ! *
* *
******************************************
Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...
description size overlap FDR database
1 Isaacs Syndrome 55 5 0.001525439 disease_GLAD4U
2 Atrial Fibrillation 52 4 0.022003754 disease_GLAD4U
3 Atrioventricular block NOS 22 3 0.031360061 disease_GLAD4U
userId
1 SCN10A;GNB4;NKX2-5;CCND2;KLF12
2 PRRX1;SCN10A;NKX2-5;CAV1
3 SCN10A;NKX2-5;POPDC3
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.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_3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 svglite_1.2.2 lattice_0.20-38 assertthat_0.2.1
[5] rprojroot_2.0.2 digest_0.6.29 foreach_1.5.1 utf8_1.2.2
[9] R6_2.5.1 plyr_1.8.6 RSQLite_2.2.8 evaluate_0.14
[13] httr_1.4.2 ggplot2_3.3.5 highr_0.9 pillar_1.6.4
[17] gdtools_0.1.9 rlang_0.4.12 curl_4.3.2 data.table_1.14.2
[21] whisker_0.3-2 jquerylib_0.1.4 blob_1.2.2 Matrix_1.2-18
[25] rmarkdown_2.11 apcluster_1.4.8 labeling_0.4.2 readr_2.1.1
[29] stringr_1.4.0 igraph_1.2.10 bit_4.0.4 munsell_0.5.0
[33] compiler_3.6.1 httpuv_1.5.1 xfun_0.29 pkgconfig_2.0.3
[37] htmltools_0.5.2 tidyselect_1.1.1 tibble_3.1.6 codetools_0.2-16
[41] fansi_0.5.0 withr_2.4.3 tzdb_0.2.0 crayon_1.4.2
[45] dplyr_1.0.7 later_0.8.0 grid_3.6.1 jsonlite_1.7.2
[49] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.1 git2r_0.26.1
[53] magrittr_2.0.1 scales_1.1.1 vroom_1.5.7 stringi_1.7.6
[57] cachem_1.0.6 farver_2.1.0 reshape2_1.4.4 doRNG_1.8.2
[61] fs_1.5.2 promises_1.0.1 doParallel_1.0.16 ellipsis_0.3.2
[65] generics_0.1.1 vctrs_0.3.8 rjson_0.2.20 iterators_1.0.13
[69] tools_3.6.1 bit64_4.0.5 glue_1.5.1 purrr_0.3.4
[73] hms_1.1.1 rngtools_1.5.2 parallel_3.6.1 fastmap_1.1.0
[77] yaml_2.2.1 colorspace_2.0-2 memoise_2.0.1 knitr_1.36