Last updated: 2024-09-16

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Knit directory: rss-gsea/

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Table legends

Prioritization results are summarized by the following table.

  • P1: posterior probability that at least one SNP within 100 kb of the transcribed region of a given pathway gene (defined by Chr., Start and End columns) has non-zero effect on the trait of interest;

  • H-distance: the physical distance, in base pair, between a given pathway gene and its nearest GWAS hit;

  • Nearest hit: the nearest GWAS hit to a given pathway gene, reported in the corresponding GWAS publication.

The “Inf” values in column H-distance indicate that there is no GWAS hit on the same chromosome as the pathway gene.

Differences between Baseline P1 and Enrichment P1 reflect the influence of enrichment on genetic associations, which can help identify putatively trait-associated genes.

Analysis results

Gene Chr. Start End Baseline P1 Enrichment P1 H-distance Nearest hit
PIK3R1 5 67511584 67597649 0.0061231 0.1365153 Inf none
MAPK9 5 179660594 179719071 0.0030671 0.0768849 Inf none
RIPK2 8 90769975 90803292 0.0013663 0.0382700 Inf none
SQSTM1 5 179233388 179265078 0.0013773 0.0378772 Inf none
IKBKB 8 42128820 42190171 0.0010981 0.0315438 Inf none
E2F1 20 32263292 32274210 0.0003299 0.0095687 Inf none
MYD88 3 38179969 38184513 0.0004038 0.0117320 99914648 chr3:138099161:I
RHOA 3 49396578 49449526 0.0567211 0.3148927 88649635 chr3:138099161:I
NTF3 12 5541280 5604465 0.0034544 0.0934039 84404494 rs2681472
YWHAE 17 1247834 1303556 0.0011822 0.0332423 57709932 rs7212798
PRKCZ 1 1981909 2116834 0.0038050 0.0827258 53379205 rs11206510
TP53 17 7571720 7590863 0.0013882 0.0392447 51422625 rs7212798
SMPD2 6 109761931 109765122 0.0009334 0.0267662 51240488 rs55730499
NDN 15 23930554 23932450 0.0018862 0.0518282 43523180 rs56062135
PIK3CA 3 178866311 178952500 0.0013510 0.0382407 40767150 chr3:138099161:I
CASP9 1 15818769 15851285 0.0021558 0.0565075 39644754 rs11206510
BAD 11 64037300 64052176 0.0011229 0.0320115 39621101 rs2128739
NDNL2 15 29560353 29562020 0.0026197 0.0632409 37893610 rs56062135
CASP6 4 110609785 110624629 0.0005801 0.0168107 37656372 rs4593108
PRKCI 3 169940220 170023770 0.0009851 0.0282127 31841059 chr3:138099161:I
OMG 17 29621668 29624380 0.0004705 0.0135788 29389108 rs7212798
MAPK10 4 86936276 87281375 0.0031026 0.0847502 29097693 rs17087335
CASP3 4 185548850 185570629 0.0009254 0.0265402 28908962 rs72689147
TRAF6 11 36505317 36531863 0.0022531 0.0622509 26754121 rs10840293
PSEN1 14 73603143 73690399 0.0016403 0.0463072 26455311 rs10139550
BCL2L11 2 111878491 111926022 0.0029726 0.0776009 26090316 rs7568458
ARHGDIA 17 79825597 79829282 0.0000666 0.0019454 20812109 rs7212798
BDNF 11 27676440 27743605 0.0036115 0.0816696 17925244 rs10840293
ZNF274 19 58694396 58724927 0.0040560 0.0949799 13271450 rs4420638
RAC1 7 6414126 6443598 0.0045409 0.0913234 12605790 rs2107595
NGFR 17 47572655 47592382 0.0221130 0.2454578 11421106 rs7212798
RTN4 2 55199325 55277734 0.0018285 0.0515254 11125199 chr2:44074126:D
DIABLO 12 122692209 122712068 0.0212340 0.1751602 10632652 rs11065979
ADAM17 2 9629392 9695917 0.0190154 0.2500008 10246556 rs16986953
MAG 19 35782989 35804710 0.0011597 0.0331098 9618236 rs4420638
PSENEN 19 36236494 36237903 0.0022393 0.0586256 9185043 rs4420638
APAF1 12 99039078 99129211 0.0010003 0.0288296 9030119 rs2681472
APP 21 27252861 27543446 0.0029699 0.0805228 8050381 rs28451064
CYCS 7 25158270 25164980 0.0012544 0.0359213 6108882 rs2107595
NGF 1 115828537 115880857 0.0052943 0.1316652 6011345 rs7528419
NCSTN 1 160313063 160328742 0.0012257 0.0347528 5917117 rs6689306
MAPK8 10 49609687 49643183 0.0017009 0.0457901 5128876 rs1870634
AKT1 14 105235686 105262080 0.0003033 0.0088363 5089976 rs10139550
RTN4R 22 20228938 20255816 0.0007157 0.0206157 4403042 rs180803
APH1A 1 150237799 150241532 0.0013969 0.0434460 4154414 rs6689306
NTF4 19 49564397 49567124 0.0005249 0.0152348 4141451 rs4420638
PRDM4 12 108126643 108154914 0.0020135 0.0530902 3904643 rs11065979
APH1B 15 63569749 63601325 0.0008176 0.0236189 3854305 rs56062135
CHUK 10 101948124 101989344 0.0043722 0.1132942 2615572 rs11191416
FURIN 15 91411885 91426687 0.6936734 0.9857790 1837667 rs8042271
MMP7 11 102391239 102401478 0.0019175 0.0540789 1271799 rs2128739
MMP3 11 102706528 102714342 0.4271857 0.9734602 958935 rs2128739
SHC1 1 154934774 154946959 0.0666216 0.3409735 538828 rs6689306
SORT1 1 109852187 109940563 1.0000000 1.0000000 34995 rs7528419
PLG 6 161123225 161175086 1.0000000 1.0000000 15081 rs2315065 

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Sonoma 14.6.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2024-09-16
 pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version    date (UTC) lib source
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 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

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