Gene Co-expression network portal 10-18-2014d1303
2015-01-13Gene Co-expression network portal 10-18-2014d1303
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 ...
- 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