Definition of key terms
REGULON PAGE:
Regulon Cytoscape Network:
Cytoscape network of causal flows connected to this regulon. Influences from mutations (green diamonds) to regulators (blue triangles) and then from regulators to the given regulon (red square) are indicated with colored edges. Red-colored edges denote up-regulation or activation while green colored edges represent down-regulation or repression.
Regulon Summary Table:
Regulons are regulatory units consisting of a coherently expressed set of genes and the associated regulator(s) whose binding site(s) they share. Regulon summary table displays all associated information related to the specific regulon including the number of genes in the regulon, Hazard ratio, its Regulator, the Transcriptional Program that includes the regulon, Drugs that are associated with members of the regulon, together with mechanism of action and class, and enriched hallmarks of cancer if any.
Regulon Genes Table:
List of genes that are included in the regulon. These genes have similar expression profiles in subset of patients and they share common binding motif for the <code> Regulator </code> of the regulon. Clicking on the gene name will take you to the gene specific page with more details. Please wait while information is collated from several resources after you click.
Causal Flows:
Causal Flows are statistically significant links between putative causal events (somatic mutations, copy number variations, chromosomal translocations, etc.) and the activity levels of regulators and regulons. In the causal flow, a mutation may causally activate or deactivate a downstream regulator which then might up- down-regulates a regulon that contains genes with similar expression profiles and binding sites.
Regulon Survival Plots:
Kaplan-Meier curves demonstrating the sub-stratification of clinical subtypes based upon the network activity of the most predictive individual or pair of genes as determined by the LASSO predictions
MUTATION PAGE:
Mutation Causal Flows Table:
List of causal flows influenced by the mutation.
Causal Flows are statistically significant links between putative causal events (somatic mutations, copy number variations, chromosomal translocations, etc.) and the activity levels of regulators and regulons. In the causal flow, a mutation may causally activate or deactivate a downstream regulator which then might up- down-regulates a regulon that contains genes with similar expression profiles and binding sites.
Mutation Cytoscape Network:
Cytoscape network of the causal flows influenced by the mutation.
Influences from mutations (green diamonds) to regulators (blue triangles) and then from regulators to the given regulon (red square) are indicated with colored edges. Red-colored edges denote up-regulation or activation while green colored edges represent down-regulation or repression.
REGULATOR PAGE:
Regulator Annotations:
Summary of regulator annotations and link-out to annotation databases
Basic gene annotations are collected from Uniprot and displayed with links to original sources. A quick link to explore the genomic context with Uniprot Browser is available.
Regulator Causal Flows:
List of causal flows containing the regulator.
Causal Flows are statistically significant links between putative causal events (somatic mutations, copy number variations, chromosomal translocations, etc.) and the activity levels of regulators and regulons. In the causal flow, a mutation may causally activate or deactivate a downstream regulator which then might up- down-regulates a regulon that contains genes with similar expression profiles and binding sites.
Regulator Cytoscape Network:
Cytoscape network of the regulator, with upstream mutations and downstream regulons.
Influences from <code>mutations</code> (green diamonds) to this <code>regulator</code> (blue triangles) and then from the regulator to the downstream <code>regulons</code> (red square) are indicated with colored edges. Red-colored edges denote up-regulation or activation while green colored edges represent down-regulation or repression.
GENE PAGE:
Gene Details:
Summary of gene annotations and link-out to annotation databases
Basic gene annotations are collected from Uniprot and displayed with links to original sources. A quick link to explore the genomic context with Uniprot Browser is available.
Gene Regulons:
List of regulons containing the gene.
A gene can be associated with multiple causal flows as a member of multiple regulons
Specific terms
Regulators: Transcription factors, miRNAs or epigenetic factors that modulate the activity of the target genes.
Nomenclature: Regulator Name
Regulon: A regulatory unit consisting of a coherently expressed set of genes and the associated regulator(s) whose binding site(s) they share.
Nomenclature: R-xxxxx
Causal Mechanistic Flows: Statistically significant links between putative causal events (somatic mutations, copy number variations, chromosomal translocations, etc.) and the activity levels of regulators and regulons.
Co-expression Clusters: Group of genes co-expressed in a subset of patients
Transcriptional Programs: Clusters of regulons that have similar activity across patient samples
