Input: Region-Centric Summary Data
Completed on: Mon May 27 11:15:13 2024 (Asia/Shanghai), with the runtime of (7 seconds).
An interactive table for user-input genomic regions (n=1133, being processed for identifying linked genes with the evidence
nearby, followed by subnetwork analysis usingSTRINGmm_finas well as subnetwork-based effect-by-removal analysis). This table has four columns: with 1st columnInput GRfor input genomic regions in the format ofchr:start-end(genome buildmm10), 2nd columnChromosomefor the chromosome, 3rd columnLengthfor the region length (bp), 4nd columnPvaluefor use-input significance information. This table can be downloaded into an excelxlsxfile.
Output: Linked Genes
Linked Gene table contains information on genes (n=2347, linked from the 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 excelxlsxfile detailing linked genes.
Evidence table displays information about the genomic regions (listed under the column
GR) that overlap the input genomic regions (listed under the columnInput GR). The overlapped regions are used to define linked genes (listed under the columnLinked genes) based on the evidence provided (see the columnEvidence). The columnEvidenceindicates the datasets used, such asProximityfor genomic regions in proximity, and the prefixEP_for enhancer-promoter map datasets. Also available for download is an excelxlsxfile for details on the linking evidence.
Output: Gene Subnetwork
A network visualisation of the subnetwork, with
31genes/nodes color-coded by linked gene scores (ranged from 1 to 10). An editable pdf file is also available for download.
Figure 1: Visualisation of the subnetwork, with genes/nodes color-coded by linked gene scores (ranged from 1 to 10).
An interactive table for the
31subnetwork genes, with the columnGScoresfor linked gene scores (ranged from 1 to 10). Also available for download is an excelxlsxfile detailing subnetwork results.
Output: Effect-By-Removal Analysis
An upset plot, visually capturing the effect of node removal. An editable pdf file is also available for download.
Figure 2: An upset plot illustrating the fraction of disconnected nodes on the y-axis against node removal (indicated by solid circles beneath) on the x-axis.
An interactive table for the
31subnetwork genes, with the columnFraction of nodes disconnecteddescribing the fraction of nodes disconnected upon the node removal (see the columnRemoved). Also available for download is an excelxlsxfile detailing effect-by-removal results.