1. SNP data
  2. Gene data
  3. Co-expression data
  4. eQTL data
  5. Pascal data
  6. PPI data
  7. Differential expression data
  8. BrainSpan expression pattern data
  9. BrainCloud expression pattern data
  10. WGS data of monozygotic twins discordant for SCZ
  11. Reference

SNP data

SNP data was downloaded from PGC2 which contains 9,444,230 SNPs.[1] The sample size included in the GWAS meta-analysis was 82,315, including 35,476 schizophrenia cases and 46,839 controls. RegulomeDB[2] score was introduced to annotate the SNPs. Non-synonymous (missense) variants were also annotated by SIFT[3,4] and PolyPhen-2.[5] The total data can be downloaded from PGC2

Gene data

Gene data was prioritized by the following items: (1) genes identified by GWAS;[6-23] (2)genes affected by CNVs;[24] (3)genes identified by linkage and association study;[25-27] (4)genes identified by convergent functional genomics (CFG);[28] (5)genes identified by Sherlock integrative analysis;[29-30] (6)genes identified by Pascal gene based test;[31] (7)genes expressed differentially in schizophrenia.[32-37]The prioritization of schizophrenia risk genes can be downloaded from here

Co-expression data

we performed gene co-expression analyses using RNA-seq-based expression data from the BrainSpan: Atlas of the Developing Human Brain ( BrainSpan atlas were divided into four anatomic regions and fifteen developmental stages as described in studies of Willsey et al.[38] and Gilman et al.68 The four anatomic regions are: (1) V1C-STC cluster (V1C, ITC, IPC, A1C, and STC); (2) Prefrontal and primary motor-somatosensory cortex or M1C-S1C cluster (M1C, S1C, VFC, MFC, DFC, and OFC); (3) STR-AMY cluster (STR, HIP, AMY); (4) MD-CBC cluster (MD and CBC). The fifteen developmental stages are: (1) Embryonic, from 4 to 8 postconception weeks (PCW); (2) Early fetal, from 8 to 10 PCW; (3) Early fetal, from 10 to 13 PCW; (4) Early mid-fetal, from 13 to 16 PCW; (5) Early mid-fetal, from 16 to 19 PCW; (6) Late mid-fetal, from 19 to 24 PCW; (7) Late fetal, from 24 to 38 PCW; (8) Neonatal & early infancy, from 0 to 6 months (M); (9) Late infancy from 6 to 12 M; (10) Early childhood, from 1 to 6 years (Y); (11) Middle and late childhood, from 6 to 12 Y; (12) Adolescence, from 12 to 20 Y; (13) Young adulthood, from 20 to 40 Y; (14) Middle adulthood, from 40 to 60 Y; (15) Late adulthood, more than 60 years old. Pearson correlation coefficients were calculated in each brain region across developmental stages as described previously.[38-39] Only gene pair whose Pearson correlation coefficient equal or bigger than 0.8 were retained. The whole data can be downloaded from here.

eQTL data

We downloaded genome-wide expression and genotype data from the study of Myers et al., which included 193 neuropathologically normal human brain samples.[40] The association between each SNP and transcript was assessed using PLINK,[41] as described in the study of Myers et al.[40] In total, we assessed correlations among 366,140 SNPs and the expression of 14,078 detected transcripts. Because the eQTL data is quite large, if users want to require it, please cantact us!

Pascal data

Gene-based tests were performed for association by using Pascal.[31] SNP P-value data was downloaded from PGC2 as desciribed in "SNP data". Pascal data can be downloaded from here.

PPI data

We downloaded PPI data from InWeb, a well-characterized PPI databased developed by Lage et al.[42,43]

Differential expression data

We downloaded 5 microarray datasets (which used brain tissues from schizophrenia patients and controls) from gene expression omnibus (GEO) including GSE53987 (contains three brain tissues: pre-frontal cortex, striatum and hippocampus; a total of 114 samples),[32] GSE12649 (prefrontal cortex; a total of 69 postmortem brains samples),[33] GSE21138 (prefrontal cortex; a total of 59 postmortem brains samples),[34] GSE35978 (cerebellum and parietal cortex brain; a total of 195 samples),[35] and GSE62191 (frontal cortex; a total of 59 samples).[36] We re-analyzed these microarray datasets and top 1 differentially expressed genes in schizophrenia cases and controls were integrated into SZDB. In addition, differentially expressed genes identified by RNA sequencing[37] were also integrated into SZDB. Differential expression data can be downloaded from here

BrainSpan expression pattern data

As desciribed in "Co-expression data", BrainSpan atlas were divided into four anatomic regions and fifteen developmental stages.

BrainCloud expression pattern data

BrainCloud[44] PFC expression data was also divided into fifteen developmental stages, as described in "Co-expression data".

WGS data of monozygotic twins discordant for SCZ

de novo mutations data identified by whole-genome sequencing of monozygotic twins discordant for schizophrenia can be download from here. More details please refer to the original aricle Tang J, et al,. 2017. Journal of Genetics and Genomics[45].


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