We screened the whole ArrayExpress database and downloaded whole transcript microarray experiment datasets related with folliculogenesis from 18 mouse models by using Affymetrix GeneChip Mouse Genome 430 2.0 platform.
Microarray experiments (dataset VIII) were performed with custom UNC Agilent two-channel microarrays.
Consequently, 80 human, mouse and rat microarray experiments (datasets) from Gene Expression Omnibus (GEO) database met the selection criteria.
Basing on the microarray experiment (the datasets that we chose from GEO were from good quality and already normalized) the fold change between the two conditions can be computed for each gene.
In our study, we were only able to obtain the negative interaction data from a microarray experiment although the dataset had an imbalanced problem.
Along the attempts to search large public microarray databases at experiment dataset level, individual gene expression profile level search method has also been conceptualized and developed [ 8].
A detailed description of the microarray experiment, together with the resulting dataset, is available at NCBI's Gene Expression Omnibus (GEO [ 17, 18], http://www.ncbi.nlm.nih.gov/geo) using the accession numbers GPL5972 (the used microarray) and GSE14396 (data).
All datasets in this study were published within the past 5 years (2004-2009) and following the Minimum Information about a Microarray Experiment (MIAME) guidelines, including 49 datasets, with 3,832 samples containing 16, 15, 11, and 7 datasets from colon, liver, lung and thyroid cancer, respectively (Additional file 1: Table S2).
Data were downloaded in May 2005 (dataset 1), covering 1,823 microarray experiments, and in April 2006 (dataset 2, an update including dataset 1) covering 2,202 microarrays.
