SNP-rich gene expression hubs, connecting myelin-related and synaptic dysfunction in schizophrenia.
Description
Stable 1: Summary information for all genes with positively correlating genes based on expression data in the Allen Brain Atlas [2, 3]. Pairwise gene expression correlations taken from [4]. Differential methylation values in schizophrenic patients were taken from [1] and summed up for the "correlation neighbors" (i.e. genes having a Pearson correlation of min. 0.8) of each gene. References 1. Wockner LF, Noble EP, Lawford BR, Young RM, Morris CP, Whitehall VL, Voisey J: Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients. Transl Psychiatry 2014, 4:e339. 2. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL et al: An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 2012, 489(7416):391-399. 3. Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K et al: Transcriptional landscape of the prenatal human brain. Nature 2014, 508(7495):199-206. 4. Wu Y, Yao YG, Luo XJ: SZDB: A Database for Schizophrenia Genetic Research. Schizophr Bull 2016.
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Steps to reproduce
1. Count the number of correlating genes (pairwise correlations taken from http://www.szdb.org/download.html#coexpression ) for each of the ~20k genes in table. This appears as column 11 in Stable 1, called geneOcc in the 1st row of the table. 2. Count how many of the correlating genes are hypomethylated. This appears in column 2, called pairs_hypometh. 3. Count how many of the correlating genes are hypermethylated. This appears in column 3, called pairs_hypermeth. 4. Count the number of hypomethylated probes of genes in column 2, shown in column 4, called pairs_hypoSum. 5. Count the number of hypomethylated probes of genes in column 3, shown in column 5, called pairs_hyperSum. 6. Show if the gene promoter or cis region (1p or 1c, respectively) appears in [1], in column 12, called 108prom/cis. Reference 1. Schizophrenia Working Group of the Psychiatric Genomics, C. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421-427, doi:10.1038/nature13595 (2014).