Sentence examples for pathways collected from from inspiring English sources

Two different collections of gene sets were used, that can be downloaded from the MSigDB website http://www.broad.mit.edu/gsea/msigdb/index.jsp: MSigDB C2 CP collection, composed of pathways collected from various sources such as online databases, biomedical literature in PubMed, and knowledge of domain experts.

EuGene relies on 2 components, (i) a database of consistently annotated pathways collected from a number of state of the art pathway resources and (ii) a module of computation implementing an array of tailored heuristics and statistical methods.

KEGG pathway maps are manually drawn reference pathways collected from published literature.

Connections between these pathways collected from KEGG database and graphs [ 24] are represented by arrows plus edges.

The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases.

Genes are either breast cancer related [ 19] or involved in estrogen signaling pathways collected from Ingenuity Pathway Analysis (Ingenuity® Systems, http://www.ingenuity.com).com

ConsensusPathDB and Pathway Commons contain pathway data collected from publicly available pathway databases (e.g., Reactome [ 26], KEGG [ 27]; see the respective homepages for more information).

In this framework, many known pathways are collected from literatures to construct a combined pathway, named 'reference pathway', which only considers chemical transformations without distinguishing the difference of organisms (Fig. 1A, left).

Metabolic genes, enzymes and pathways were collected from AraCyc, a biochemical pathway database for Arabidopsis [ 5] (Additional file 8: Table S7).

All the cancer-related pathways were collected from Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database and listed in Table 1.

Genes involved in nicotine pathways were collected from previous studies [ 26- 32].