Genes identified by Sherlock integrative analysis

Symbol LBFa P-valueb Supporting SNPc PeQTLd PGWASe FDRf LocusZoom
ZNF3237.092.22 × 10-6rs2859365 (cis)5.90 × 10-82.07 × 10-73.69 × 10-3
NAPSA7.042.22 × 10-6rs10226475 (trans)6.74 × 10-62.02 × 10-103.69 × 10-3
LOC3781356.762.22 × 10-6rs134169 (trans)6.17 × 10-62.50 × 10-53.69 × 10-3
EPB41L26.662.22 × 10-6rs7752195 (trans)1.17 × 10-51.82 × 10-53.69 × 10-3
GLT8D15.834.43 × 10-6rs2240920 (cis)5.22 × 10-167.30 × 10-67.35 × 10-3
RCN15.834.43 × 10-6rs3800917 (trans)6.56 × 10-76.27 × 10-107.35 × 10-3
ALMS15.561.11 × 10-5rs6753344 (cis)1.37 × 10-95.00 × 10-51.84 × 10-2
EIF4A25.391.11 × 10-5rs17002034 (trans)4.00 × 10-71.40 × 10-61.84 × 10-2
MPV17L25.301.11 × 10-5rs7752195 (trans)1.54 × 10-61.82 × 10-51.84 × 10-2
LSAMP5.131.11 × 10-5rs4976976 (trans)4.53 × 10-76.23 × 10-61.84 × 10-2
CSNK2B5.111.11 × 10-5rs707939 (cis)5.35 × 10-68.23 × 10-71.84 × 10-2
PLCD45.091.55 × 10-5rs2160567 (trans)7.40 × 10-78.29 × 10-62.57 × 10-2
Symbol LBFa P-valueb Supporting SNPc PeQTLd PGWASe FDRf LocusZoom
Note:
aLBF (Log Bayes Factors for each gene) evaluates whether the combined evidence from GWAS and expression studies support a gene being associated with schizophrenia. For example, a LBF of 4.6 means that the alternative hypothesis (associated with Schizophrenia) is 100 times (exp[4.6] = 100) more likely than the null hypothesis (no association). High Bayes factors tend to correlate with low P-values. Several eSNPs may be associated with the expression of a gene. For each of these eSNP, if it is also associated with schizophrenia in GWAS, a positive score would be given; otherwise, a negative score. Association only in GWAS (ie, non-eSNPs) does not alter the score. The total score of a gene increases with the number of SNPs with combined evidence (SNPs that are associated with schizophrenia and expression). For each gene, Sherlock computes individual LBFs for each SNP pair in the alignment, and the sum of these constitutes the final LBF score for the gene.
bP-value from Sherlock integrative analysis.
cSNP with the highest LBF score.
dP-value for eQTL SNP from the study of Myers et al. 2007.
eP-value for eQTL SNP from the study of Ripke et al. 2013.
fFDR was calculated at P = 10–5 threshold. It should be noted that some genes with different LBF scores may have the same P-values. This is because that Sherlock computes P-values by finite permutations. If the number of permutation is not extremely high, it is possible that two different values of LBF correspond to the same P-values (their rankings are the same). Genes with LBF > 5.0 and P-value < 10–4 are listed.

Data source: Luo et al. Systematic integration of brain eQTL and GWAS identifies ZNF323 as a novel schizophrenia risk gene and suggests recent positive selection based                    on compensatory advantage on pulmonary function. Schizophrenia Bulletin, 41(6): 1294-1308(2015).

Copyright © 2015-2017 Kunming Institute of Zoology, Chinese Academy of Sciences. All Rights Reserved.