Input into cTGene

Completed at Sat Apr 30 00:12:25 2022 (Asia/Shanghai), with the runtime of 93 seconds on the server side (not including the runtime on the client/user side).

An interactive table of user-defined SNPs, with 1st column SNPs for dbSNP rsIDs, 2nd column P-values for significance info.

Output: target genes

Manhattan plot illustrates priority rating for target genes that are color-coded by chromosomes, with the top 30 target genes labelled. Also provided is an editable PDF file for download.

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Manhattan plot illustrating priority rating (y-axis) for target genes (color-coded by chromosomes; x-axis), with top target genes labelled.

Figure 1: Manhattan plot illustrating priority rating (y-axis) for target genes (color-coded by chromosomes; x-axis), with top target genes labelled.

Prioritisation table for targets at the gene level, each receiving 5-star priority rating (scored 0-5; see the column Rating) and its rank (see the column Rank). The prioritised target genes are cross-referenced and hyperlinked to GeneCards; see the column Genes. The column Type tells the target gene type (either Core for core genes or Peripheral for peripheral genes). Also provided is a summary of evidence used to define core genes, including columns Proximity (evidence of genomic proximity), QTL (e/pQTL evidence) and PCHiC (conformation evidence). For details on evidence, please refer to Evidence table.

Evidence table for core genes, showing which SNPs (see the column SNPs) are used to define core genes (the column Core genes) based on which evidence (see the column Evidence). The column SNP type tells the SNP type (either Input for use-input SNPs or LD for LD SNPs). Notably, the column Evidence details datasets used: the prefix Proximity_ indicative of SNPs in the proximity, the prefix PCHiC_ for PCHi-C datasets, and the prefix QTL_ for e/pQTL datasets.