Input Genomic Region Information

Completed on Sun Apr 09 21:19:02 2023 (Asia/Shanghai), with the runtime of 21 seconds.

An interactive table for user-input genomic regions (n=381, being processed). The table includes three columns: 1st column Input GR for input genomic regions in the format of chr:start-end (the genome build hg19), 2nd column Chromosome for the chromosome, 3rd Length for the region length (bp).

Output: Linked Genes

Linked Gene table contains information on genes (n=408, linked from input genomic regions), including the column GScores (ranged from 1 to 10) that quantifies the degree to which genes are likely modulated by input genomic regions. 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 about the genomic regions (listed under the column GR) that overlap the input genomic regions (listed under the column Input GR). The overlapped regions are used to define linked genes (listed under the column Linked genes) based on the evidence provided (see the column Evidence). The column Evidence indicates the datasets used, such as Proximity for genomic regions in proximity, the prefix PCHiC_ for promoter capture Hi-C datasets, and the prefix ABC_ for enhancer-gene map (ABC) datasets.

Output: Enriched Terms

An interactive table that displays enriched ontology terms based on 408 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.

DOWNLOAD .pdf
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.

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

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