Table indicates annotation of GO functional terms based on Biological Process ontology for the selected gene. Id is identifier of the functional term in the database; Description is name of the functional term.
[[item.ID]]
[[item.Description]]
No annotations found!
Table indicates annotation of GO functional terms based on Molecular Function ontology for the selected gene. Id is identifier of the functional term in the database; Description is name of the functional term.
[[item.ID]]
[[item.Description]]
No annotations found!
Table indicates annotation of GO functional terms based on Cellular Component ontology for the selected gene. Id is identifier of the functional term in the database; Description is name of the functional term.
[[item.ID]]
[[item.Description]]
No annotations found!
Table indicates annotation of KEGG pathways for the selected gene. Id is identifier of the functional term in the database; Description is name of the functional term.
[[item.ID]]
[[item.Description]]
No annotations found!
Table indicates TFs that target the selected gene based on TRANSFAC annotation. Transcription Factor is name of the TF; Description is description of the TF; and Type of Regulation is type of regulation (activation, repression, or unknown) indicated in the database.
[[item.TranscriptionFactor]]
[[item.Description]]
[[item.TypeOfRegulation]]
No annotations found!
Table indicates miRNA families that target the selected gene based on TargetScan 6.2 annotation. miRNA family is name of the miRNA family; miRNAs lists miRNAs included in the family.
[[item.miRNAFamily]]
[[item.miRNAs]]
No annotations found!
Dynamic network showing gene co-expression network for the selected endometrial profile. Nodes (in grey) represent genes and edges represent Pearson’s correlation. Positive correlations are shown in green and negative correlations are shown in red with a variable width depending on the Pearson correlation value (R2). R2 is filtered to better network visualization. Edges into modules are filtered if their correlation value is lower than 0.5 (preserving the modules obtained from the WGCNA) and edges between modules are shown if their R2 value is higher than, 0.75.
Heatmap represents correlation matrix values for every gene pair. Gradient colors depend on Pearson correlation values, from green (positive correlation, R2 > 0) to white (no correlation, R2 = 0) and from white to red (negative correlation, R2 < 0). Black rectangles indicate co-expression modules. This heatmap can be downloaded (.JPG format) using the export button.
Network Parameters & Key Drivers
Network Parameters
[[item.g]]{{_computeKeyDriver2(item.g)}}
[[item.d]]
[[item.bc]]
[[item.cc]]
Table shows results for transcription factor (TF) enrichment using the Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST) webtool for genes in the considered module. Key TF indicates name of the TF; Description indicates the TF description; No. genes indicates number of target genes for this TF in the considered module; P-value is the p-value for enrichment analysis; FDR is the false discovery rate-corrected p-value; and Genes lists target genes for this TF in the considered module.
[[item.tf]]
[[item.description]]
[[item.num_overlapped_genes]]
[[item.p_value]]
[[item.fdr]]
[[item.list_of_overlapped_genes]]
Table shows enrichment results for miRNA families using the miRNA binding site over-representation (mBISON) webtool for genes belonging to the considered module. miRNA family indicates name of the miRNA family; miRNAs indicates miRNAs included in the miRNA family; No. genes indicates number of target genes for this miRNA family in the considered module; P-value is the p-value for enrichment analysis; FDR is the false discovery rate-corrected p-value; and Genes lists target genes for this miRNA family in the considered module.
[[item.miR_Family]]
[[item.miRNAs]]
[[item.times_found_in_3_UTRs]]
[[item.p_value_for_over_representation]]
[[item.FDR_for_over_representation]]
[[item.genes]]
Functional Groups - Biological Process
TTable shows results for functional enrichment considering manually defined functional groups based on Biological Process ontology included in the Gene Ontology (GO) database. Enrichment was done using Fisher exact test followed by false discovery rate (FDR) correction for multiple testing. Functional Group is name of the functional group; Gene Ratio indicates number of genes in the module that are included in the functional group over total number of genes in the module that are included in at least one functional group; Bg Ratio indicates number of genes included in the functional group over the total number of considered genes; P-value is the p-value for enrichment analysis; FDR is the FDR-corrected p-value; and Genes lists the target genes for this miRNA family in the considered module.
[[item.Description]]
[[item.GeneRatio]]
[[item.BgRatio]]
[[item.pvalue]]
[[item.padjust]]
[[item.geneID]]
Functional Groups - Molecular Function
Table shows results for functional enrichment considering manually defined functional groups based on Molecular Function ontology from the GO database. Enrichment was done using Fisher exact test followed by FDR correction for multiple testing. Functional Group is name of the functional group; Gene Ratio indicates number of genes in the module that are included in the functional group over total number of genes in the module that are included in at least one functional group; Bg Ratio indicates number of genes included in the functional group over total number of considered genes; P-value is the p-value for enrichment analysis; FDR is the FDR-corrected p-value; and Genes lists target genes for this miRNA family in the considered module.
[[item.Description]]
[[item.GeneRatio]]
[[item.BgRatio]]
[[item.pvalue]]
[[item.padjust]]
[[item.geneID]]
Functional Groups - Cellular Component
Table shows results for functional enrichment considering manually defined functional groups based on Cellular Component ontology from the GO database. Enrichment was done using Fisher exact test followed by FDR correction for multiple testing. Functional Group is name of the functional group; Gene Ratio indicates number of genes in the module that are included in the functional group over total number of genes in the module that are included in at least one functional group; Bg Ratio indicates number of genes included in the functional group over total number of considered genes; P-value is the p-value for enrichment analysis; FDR is the FDR-corrected p-value; and Genes lists target genes for this miRNA family in the considered module.
[[item.Description]]
[[item.GeneRatio]]
[[item.BgRatio]]
[[item.pvalue]]
[[item.padjust]]
[[item.geneID]]
Table shows results for functional enrichment considering manually defined functional groups based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database. Enrichment was done using Fisher exact test followed by FDR correction for multiple testing. Functional Group is name of the functional group; Gene Ratio indicates number of genes in the module that are included in the functional group over the total number of genes in the module that are included in at least one functional group; Bg Ratio indicates the number of genes included in the functional group over the total number of considered genes; P-value is the p-value for enrichment analysis; FDR is the FDR-corrected p-value; and Genes lists target genes for this miRNA family in the considered module.
[[item.Description]]
[[item.GeneRatio]]
[[item.BgRatio]]
[[item.pvalue]]
[[item.padjust]]
[[item.geneID]]
Dynamic network shows gene co-expression network for the selected endometrial profile and enriched regulators (TFs and miRNAs) for each module. Grey rounded nodes represent genes, black diamonds represent enriched TFs, and black rectangles represent enriched miRNA families. Edges representing Pearson’s correlation are green (positive correlation, R2 > 0) or red (negative correlation, R2 < 0), with a variable width depending on the value. R2 is filtered to better visualize the network. Edges into modules are filtered if R2 < 0.5 (preserving modules obtained from WGCNA), and edges between modules are shown if R2 > 0.75. Grey dashed edges represent relations between a regulator and its target gene.
[[item.miRNA_Family]]
[[item.times]]
[[item.p_value]]
[[item.FDR]]
[[item.name]]
[[item.desc]]
[[item.genes]]
[[item.pvalue]]
[[item.FDR]]
[[item.overlapped]]