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As a first step in this process, raw.cel files from the AtGenExpress dataset were downloaded and analyzed for differential expression.
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Sequence datasets were downloaded and processed as described below.
Five datasets were downloaded and used in this study.
The leukocyte (GSE1133 & GSE22886), mouse AS (GSE41039) and patient biopsy (GSE41038) datasets were downloaded and processed independently [ 14– 17].
For mouse and rat, expression dataset were downloaded from the Mammalian Reproductive Genetics website and annotation files were obtained from Affymetrix website.
Cel files from the GSE9372 and GSE7851 dataset were downloaded from the Gene Expression Omnibus [16].
More detailed information of the ADA tool is given in [ 4]. van de Vijver dataset and TRANSBIG dataset were downloaded from the public domain.
The 3020 proteins of the core dataset were downloaded.
The gut samples of the Human Microbiome Project HMPP) dataset were downloaded as an assembly in 1,889,651 contigs [ 41].
The external colon cancer validation dataset was downloaded from http://www.affymetrix.com and consisted of 18 paired samples of adenocarcinoma and adjacent normal tissue [ 35].
The BRENDA human dataset was downloaded from the website and aligned against the human genome using BLAT.
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