Sentence examples for background set of genes from inspiring English sources

More specifically, we computed the overlap between the MolSigDB gene sets and our set of genes and compared what would be expected by chance if equivalent number of genes were drawn uniformly at random from the background set of genes.

The mouse genome was used as the background set of genes and P-value correction was performed by the method of Benjamani and Hochberg [69].

The promoter regions were scanned for overrepresentation of putative cis-elements as compared with a background set of genes not known to be oscillating.

Our background set of genes was composed only of genes measured in this study.

Our background set of genes were those genes measured in our tissue samples.

This GO enrichment analysis tool allows comparing the presence of GO terms in a given gene catalogue with respect to a custom background set of genes.

An important parameter, namely Support, is the probability that the promoters D contain a TFBS A or the combinatorial TFBSs A and B. After the co-occurrences of TFBSs in the group of gene promoter sequences have been mined, the statistical significance of each TFBS should be examined against the background set of gene promoters, based on the hypergeometric equation (p-value) [ 4].

Thus, we composed background sets of genes with unaltered expression in the tumor state to adjust score cut-offs.

We tested this hypothesis by comparing the distributions of expression variance between genes containing promoter region TRs against background sets of genes lacking promoter region TRs that are either from the same genomic region or have the same functional annotation.

In the second comparison, to control for biases due to gene function, we compared the set of TR-containing loci against 10 different random background sets of genes that have the same functional classifications according to the FunCat Annotation Database (Ruepp et al. 2004).

For each trait dataset the R [ 18] package GOseq [ 19], without the correction for gene length bias, was used to identify the KEGG pathways which were significantly over-represented (p < 0.05) by the set of genes compared against the background set of human genes.