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The properties evaluated were: release authority (who decides the release content), versioning (what is the scheme to name the release versions), pre-release testing, approval of releases (who approves a the software is ready to be released), distribution (how the software is distributed), and formats (in which formats the software is released).
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Pathways associated with differentially expressed genes identified by our proposed algorithm and SAM were analyzed using the Tox Analysis function in IPA (Ingenuity Systems, Redwood City, CA) [Application version: 8.0, Build: 82437; Content version: 2602].
The three functional genomic approaches included: Ingenuity® Functions, Diseases and Canonical Pathways Analysis: Functional analysis was done with Ingenuity® Pathways Analysis (Ingenuity® Systems, www.ingenuity.com, Application version 8.6, Content version 3003).
Lists of differential genes were imported into Ingenuity IPA (Ingenuity Systems, [ 46], content version 12710793) for pathway analysis.
The functional classification of transcripts was performed with annotations provided by Ingenuity Pathway Analysis, IPA Content Version 11904312 (2012-01-17) (IngenUSAy Systems, MoUSAain View, CA, USA).
For FACS-sorted mammary epithelial cell subpopulations both resulting lists of differential genes were imported into Ingenuity IPA (Ingenuity, content version 12710793) for pathway analysis.
Ingenuity Pathway Analysis (IPA) [ 20] version 9.0 (Release Date: 2011-03-22), Content version: 3206 (Release Date: 2011-02-11)) was used to analyse selected sets of genes in order to identify over-represented canonical pathways and networks.
Pathway analyses were performed based on all significant gene-specific probes using the Ingenuity Pathway Analysis IPAA) software tool (IPA build version: 338830 M, content version: 23814503, release date: 2015-03-22; analysis Date: 2015-06-19; http://www.com/nuity.com/).com/
