Sentence examples for background list of all from inspiring English sources

Genes with a differential expression q value less than 0.001 were compared to the background list of all genes in this analysis.

The z-score indicates the statistical significance of the overlap between gene lists (Additional file 8C) which can be determined given the background list of all Arabidopsis genes.

Enrichments were calculated by comparing the counts of TFBSs within our set of DMR-associated promoters to the number of counts occurring in a background list of all RefSeq promoters overlapped by all sampled 450 K probes.

For each of these sets of parent genes, we used the GOrilla tool with default settings to look for GO terms enriched in the set compared to the background list of all parent genes.

We then submitted the DE lists versus a background list of all genes present on the array to the GOrilla webtool [ 17], which uses hypergeometric statistics to determine functional enrichments.

A reference background list of all D. melanogaster genes orthologous to all A. mellifera RNAs was used to determine significant enrichment of BP GO terms and annotation clusters using a chi-square (X) test corrected for multiple testing [ 48].

We determined the overlap of each hot spot list with the background list of 55 003 regions.

The background list comprised all of the genes for the miRNA-mRNA pairs that we obtained from Tarbase 6.0.

We used the following parameters: organism, human (hg19); regulatory element type, protein-coding genes; ID type, symbol; background regions, a list of all genes assessed across all 10 discovery data sets; analysis window center, TSS/5′ end (transcription start site); upstream and downstream window size relative to TSS, 500 bp; and cell lines, all.

For statistical analysis, all analyzed proteins in this study (unique IDs) were set as the background list and all pathways consisting of more than five proteins from the background list were considered for statistical analysis by Fisher's exact test, resulting in a total of 93 pathways from PID and 63 from KEGG.

A list of unranked significantly up- and down-regulated genes was compared to a background list containing all C.  elegans genes expressed in our RNA-seq samples.