Network data from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011)Bioinformatics, 27 (13). pp. 1860-1866.

Gillis, J., Pavlidis, P. (2011) Network data from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011)Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

	Other (protein-protein interaction network (PPIN) (MatLab)) ppin.mat - Published Version Available under License Creative Commons Attribution. Download (554kB)
	Other (Yeast PPIN (MatLab)) yeast_ppin_ex.mat - Published Version Available under License Creative Commons Attribution. Download (312kB)
	Other (Experiment IDs in Bias exps ID) biasexps.mat - Published Version Available under License Creative Commons Attribution. Download (383B)

Abstract

The coexpression is very large and can be regenerated more easily than transferred (or saved, for individual expression experiments). The expression data can be accessed at: http://www.chibi.ubc.ca/Gemma/expresionExperiment/showExpressionExperiment.html?id=### where “###” is the experiment number given, e.g., 149 with experiment IDs in Bias exps ID The networks can be generated using: Read raw expression data Coexpression matrix calculator These files call Gemma but will first check if the expression data has already been saved, so the data can be downloaded from the links above directly, with a bit of a look to ensure formatting is OK (with appropriate directory changes, etc). The expression web pages also have sparse coexpression links for most experiments, from which an aggregated sparse network could be constructed which is very similar to aggregating un-thresholded data, as discussed in the paper. However, the paper used the underlying data directly to construct the aggregate sparse network.

Item Type:	Dataset
Subjects:	bioinformatics bioinformatics > genomics and proteomics > computers bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
CSHL Authors:	Gillis, Jesse
Communities:	CSHL labs > Gillis Lab
Depositing User:	Matt Covey
Date:	2011
Date Deposited:	29 Apr 2013 19:04
Last Modified:	29 Apr 2013 19:04
Related URLs:	Author
URI:	https://repository.cshl.edu/id/eprint/28282

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