A set of family-wide shared genes was created from the homologous gene clusters output from BlastClust.
Regulatory and signaling networks of genes were created from the differentially expressed genes at the 2 hrs, 8 hrs and 24 hrs time points.
A number of studies have showed that recently created genes differ from the genes created in deep evolutionary past in many aspects.
A database of resistances genes was created from (1) all sequences in Antibiotic Resistance Database (ARDB) [48] and (2) sequences from known quinolone resistance genes consisting of sequences from qnrA-D, qnrS, qepA, acrA-B, norA-C and oqxA-B [29], [32], [49].
A list of 24 617 uniquely annotated bovine genes was created from the Ensembl Biomart database [ 27, 28].
Gene lists of hypoxia-related genes were created from comparative analyses of hypoxia treated (time-points 1, 2, 4, 8 or 12 h) versus untreated (time 0 h) using limma, a R implemented package available from Bioconductor.
We determined the F. xananassa gene index and related it to different plant species using the DFCI Gene Index Database (for species like Arabidopsis thaliana, Oryza sativa or Vitis vinifera), and "ad hoc" gene indices created from the GenBank dbEST (for species like Prunus persica, Prunus armeniaca, Citrus spp. or Fragaria vesca).
Our fibroblast dataset was compared to our emphysema dataset by using a gene set created from the 100 most upregulated miR-638 predicted targets (by fold change) between miR-638 inhibitor experiments and control experiments.
Sequencing of the STS gene cDNA, created from RNA isolated from 8 of the 21 post-mortem brain samples confirmed the inclusion of the alternative exons 0a and 1b [as described by Dalla Valle et al., 2007] and exon 2 in the transcript (schematic in Fig. 4).
Metasignatures are identified by performing gene-list enrichment analyses using a transcription factor gene-set library created from the ChEA database, or a histone modification gene-set library created by processing data from the Roadmap Epigenomics.
