Input: Region Information

Completed on Sun May 26 11:44:57 2024 (Asia/Shanghai), with the runtime of 10 seconds.

An interactive table for user-input genomic regions (n=1133, being processed for identifying linked genes with the evidence nearby, followed by enrichment analysis using Fisher's exact test and the ontology GOBP). The table includes three columns: 1st column Input GR for input genomic regions in the format of chr:start-end (the genome build mm10), 2nd column Chromosome for the chromosome, 3rd Length for the region length (bp). This table can be downloaded into an excel xlsx file.

DOWNLOAD .xlsx

Output: Linked Genes

Linked Gene table contains information on genes (n=2347, 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. Also available for download is an excel xlsx file detailing linked genes.

DOWNLOAD .xlsx

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, and the prefix EP_ for enhancer-gene map datasets. Also available for download is an excel xlsx file for details on the linking evidence.

DOWNLOAD .xlsx

Output: Enriched Terms

An interactive table that displays enriched ontology terms based on 2347 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. Also available for download is an excel xlsx file detailing enrichment results.

DOWNLOAD .xlsx

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 red 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 red 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).