The annotation and distribution of distinct classes of repetitive elements associated with individual gene were collected to characterize genes in association with different types of repetitive elements using systems biology program.
In the annotation guided approach all probe signals for each condition of an annotated gene were collected into two groups Xn and Ym.
Information of single-nucleotide polymorphisms (SNPs) in each gene was collected from the HapMap database (http://hapmap.ncbi.nlm.nih.gov/).nih.gov/
Functional predictions, and information on disease- and trait-associations to the gene were collected from dbNSFP [ 10].
After classification, short reads mapped to a specific gene were collected in order to assemble them into contigs for further analysis.
Identical ESTs transcribed from each gene were collected by BLASTn search using criteria of >95% identity in a sequence >100 nucleotides in each cDNA library.
Despite this drawback the SNP data for RNASEL gene was collected from dbSNP because it houses the largest polymorphism database [ 73].
In transcriptome assemblies, all transcript variants (subgraphs), each potentially representing the same gene, are collected together and named "isogroup" by Newbler.
Information on cancer-related mutations in human Mx1 gene was collected from the Catalogue of Somatic Mutations in Cancer (COSMIC) database [ 34].
Gene symbols and gene positions for all of the 2403 genes were collected from RGD and Ensembl [ 6, 10].
