The Matched Interaction Across Tissues (MIxT) is a system designed for exploring and comparing transcriptional profiles from two or more matched tissues across individuals.
► Dumeaux V, Fjukstad B, Fjosne HE, Frantzen JO, Holmen MM, Rodegerdts E, Schlichting E, Borresen-Dale AL, Bongo LA, Lund E, Hallett M. Interactions between the tumor and the blood systemic response of breast cancer patients. PloS Comp Bio 2017,13(9):e1005680.
► Fjukstad B, Dumeaux V, Olsen KS, Lund E, Hallett M, Bongo LA. Building applications for interactive data exploration in systems biology. 8th ACM-BCB’17 Conference, Boston, Massachusetts, USA, pp. 556-561.
In a network, genes can be represented by nodes colored by their module membership. A pair of nodes is connected with an edge if there is a significant co-expresson relationship between them (topological overlap > 0.1). In both tissues, the edges that span between modules reflect natural overlaps between cellular processes enriched in modules.
To explore the system-level changes across tissues, we constructed tight coexpression gene sets (also called modules) in each tissue. MIxT enables the exploration of module content, expression profiles, and functional enrichment. Visualizes how module expression orders patients to identify clinicopathological variables associated with each module.
Displays significance of gene overlap between modules across tissues as such an overlap may suggest a very simple “mirrored” type of co-expression patterns. Visualizes expression of genes in common between modules across tissues. Displays significance of interactions between modules defined by the correlation between patient orderings induced by modules. Allows selection of a particular subtype. Visualizes expression of genes in modules interacting between tissues across all patients or within a subtype of interest.
Displays significance of associations between module expression and clinical variables. Allows selection of a particular subtype and exploration of module expression profiles of interest.
Given a gene list of interest, return modules in which the gene list is enriched for.
Search for a gene or pathway and return modules in which the gene or pathway is present or enriched. Investigate which genes are co-expressed with your gene of interest in both tissues.