Input SNP Information

Completed on Sun Apr 09 21:18:22 2023 (Asia/Shanghai), with the runtime of 46 seconds.

An interactive table for user-input SNPs (n=216, being processed). The table includes three columns: 1st column SNPs for input dbSNP rsIDs, 2nd column P-values for the significance info, and 3rd column Locus for genomic locations (the genome build hg19). Each SNP listed in the column SNPs is hyperlinked to its corresponding dbSNP page.

Output: Linked Genes

Linked Gene table contains information on genes (n=407, linked from input SNPs), including the column GScores (ranged from 1 to 10) that quantifies the degree to which genes are responsible for genetic associations. Linked genes are sorted by their linked gene scores and are hyperlinked to GeneCards for further information. Please refer to Evidence table for details on the linking evidence.

Evidence table displays information on which SNPs (see the column SNPs) are used to define linked genes (the column Linked genes) based on which evidence (see the column Evidence). The column SNP type indicates whether the SNP is an input SNP (Input) or an additional SNP in linkage disequilibrium (LD). The column Evidence contains information on the datasets used, such as Proximity (indicative of SNPs in proximity), the prefix PCHiC_ (promoter capture Hi-C datasets), and the prefix eQTL_ or pQTL_ (e/pQTL datasets).

Output: Enriched Terms

An interactive table that displays enriched ontology terms based on 407 linked genes. Each enriched term (the columns Ontology, Term ID and Term Name) has the enrichment z-score (Z-score), the enrichment significance level (FDR), odds ratio (Odds ratio) and 95% confidence intervals (95% CI), the number (Num) and list (Members) of member genes that overlap with linked genes. The table is sorted by FDR ascendingly.

Output: Dotplot

A dotplot of enriched ontology terms identified using Fisher’s exact test. An editable pdf file is also available for download.

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A dotplot of enriched ontology terms. The dots colored in dark green represent the terms with FDR < 0.05, indicating statistical significance. The top 5 significant terms (ordered by FDR ascendingly) are labelled for easier interpretation.

Figure 1: A dotplot of enriched ontology terms. The dots colored in dark green represent the terms with FDR < 0.05, indicating statistical significance. The top 5 significant terms (ordered by FDR ascendingly) are labelled for easier interpretation.

Output: Forest Plot

A forest plot of enriched ontology terms identified using Fisher’s exact test. An editable pdf file is also available for download.

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Forest plot for enriched ontology terms (ordered by odds ratio descendingly).

Figure 2: Forest plot for enriched ontology terms (ordered by odds ratio descendingly).