Sentence examples for based on gene lists from inspiring English sources

Functional annotation may be separated into two ways of analyses: a quantitative one by means of GES, which assigns scores to patients, and a qualitative one based on gene lists, which assigns a "Gene Ontology" enrichment score to a cluster representative gene list [ 49].

Of the generic SVM tools that can be trained with any topic of interest (e.g., BibGlimpse [ 12]), none allow literature ranking based on gene lists, although one does precisely the opposite, namely rank genes based on literature [ 13].

To systematically use these sources (step 1 Figure 1), we use Moksiskaan database, which allows making networks based on gene lists [ 19].

Thus far the gene expression analysis has been based on gene lists with differentially expressed single genes (where the focus is often on the most highly differentially expressed genes or on genes implicated beforehand).

Although the use of gene sets provides a first assessment based on gene lists derived from, for example, KEGG and other pathway databases, BN models will provide a more accurate and detailed analysis of the mechanistic effects of the exposure as well as a quantitative evaluation of the perturbation of each model under consideration and an overall pan-model biological impact.

GSEA was based on gene lists from the four comparisons (B10.Q versus B10.Q. Nss1, B10.Q versus B10.Q. Nss1/ Idd5, B10.Q. Nss1 versus B10.Q. Nss1/ Idd5 and B10.Q. Nss1/ Idd5-he versus B10.Q. Nss1/ Idd5-ho), with all of the genes remaining after the 'signal to noise' filtration in 'pre-processing 1'.

It is based on gene list analysis, simulations, spike-in data and re-sampling, with the intention to benefit from the specificity and advantages of each strategy.

Results based on genes lists assuming α = 0.01 did not change the qualitative outcome of our analyses (data not shown).

Using the DAVID database [ 25] to classify our signature gene list based on Gene Ontology terms, we found that 46% of the genes in this signature were significantly enriched in the "cell cycle" category (P ≤ 0.0001).

We used the Gene Ontology (GO) set (C5) and curated gene sets (C2) which included canonical pathways, and a senescence-associated gene list generated based on gene expression changes quantitated in human prostate fibroblasts [11].

Chromosomal clustering methods for co-expressed genes were based on gene order with a background gene list comprising the 13,773 genes represented on the Affymetrix microarray.