Two Affymetrix data sets were retrieved from the NCBI Gene Expression Omnibus GEOO) data repository.
RNA-Seq data sets were retrieved from the UCSC data repository site (http://genome.ucsc.edu/ [last accessed May 20, 2015]; Meyer et al. 2013) for visualization and analysis of cell type-specific transcriptional activity of defined genomic regions.
For this study, we have combined several datasets which were retrieved from public data repositories.
As the publicly available draft genome sequence of L. fermentum FTDC 8312 was not annotated, its genome sequence was retrieved from the NCBI data repository, followed by automated annotation using the GenDB platform as described above.
Two Affymetrix U133 Plus 2.0 datasets containing 58 primary adenocarcinomas of the lung (GSE3141) and 19 brain metastasis samples of primary adenocarcinomas of the lung (GSE14108) were retrieved from the NCBI Gene Expression Omnibus GEOO) data repository [ 16].
In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database.
Background normalized raw data of these beta-values were determined with the BeadStudio software (Illumina) and retrieved from the public data repositories Gene Onmibus and Array Express.
Five different data sets have been used for evaluating BITCP, and these data sets have been retrieved from GitHub repository.1 Data sets presented in Table 2 consist entirely of mathematical projects.
All known regulatory networks were retrieved from the public domain data repository, provided that such individual networks held at least one element of a given dataset.
Already reported and potentially solved problems, as well as other historical data are retrieved from a knowledge repository through advanced indexing techniques in order to support the identification of solutions for newly experienced problems.
To obtain the DEGs between the different groups of AIDS patients with different race, age, and sex backgrounds, publicly available microarray data sets were retrieved from the GEO repository using the Agilent RNA 6000 Assay Microchip technology.
