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The Matched Interaction Across Tissues (MIxT) is a system designed for exploring and comparing transcriptional profiles from two or more matched tissues across individuals.
References:
► 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.
Data:
► Laser-capture microdissected tumor epithelium and matched stroma of invasive breast cancer [GEO: GSE5847]
► Boersma BJ, Reimers M, Yi M, Ludwig JA et al. A stromal gene signature associated with inflammatory breast cancer.
Int J Cancer 2008 Mar 15;122(6):1324-32.
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.