Prioritization results of coronary artery disease & p75(NTR)-mediated signaling

Last updated: 2019-02-18

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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 3.5.2 (2018-12-20)
 os       macOS Mojave 10.14.3        
 system   x86_64, darwin15.6.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2019-02-18                  

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[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library

Prioritization results of coronary artery disease & p75(NTR)-mediated signaling

Xiang Zhu

2018-10-05

Table legends

Analysis results