Gene Co-expression network portal 10-18-2014d1303

2015-01-13

how to turn gene expression into network

basic process for turning gene expression data from multiple samples into a network
-get the gene expression values->obtain a co-expression score (use a metric like absolute value of Pearson correlation) for every pair of genes among all of the sample values and make a similarity (co-expression) score matrix->apply threshold (often a value of 0.8 is selected) so all values above value are 1, and all other values are 0 (this is the network adjacency matrix)->the network adjacency matrix could be transformed into edge list format if desired

-There's even a wikipedia article on the topic
--Gene co-expression network
--http://en.wikipedia.org/wiki/Gene_co-expression_network
--a related network is a gene regulatory network
--there are many different ways to evaluate the co-expression measure
---Pearson’s correlation coefficient is the most popular co-expression measure used in constructing gene co-expression networks
-Network visualization and analysis of gene expression data using BioLayout Express3D paper
--http://www.nature.com/nprot/journal/v4/n10/full/nprot.2009.177.html
-Network based analyses of gene expression profile of LCN2 ...
www.nature.com/srep/2014/140623/srep05403/full/srep05403.html
-Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
--http://www.biomedcentral.com/1471-2164/15/452
-Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis.
--http://www.ncbi.nlm.nih.gov/pubmed/24630964
-Reconstruction and analysis of cancer-specific gene regulatory networks from gene expression profiles
--http://arxiv.org/ftp/arxiv/papers/1305/1305.5750.pdf
-Integrative Gene Network Construction to Analyze Cancer Recurrence Using Semi-Supervised Learning
--http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086309
-Find subnetworks of differentially expressed genes
--http://www.genomespace.org/support/guides/recipes/sections/find-subnetworks-of-differentially-expressed-genes

s: gene co-expression network in young and old
-Aging mice show a decreasing correlation of gene expression within genetic modules
--http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000776#pgen-1000776-g006
-Cross-species comparison of genome-wide expression patterns paper

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