Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.
Brief Bioinform
; 20(1): 168-177, 2019 01 18.
Article
em En
| MEDLINE
| ID: mdl-28968630
ABSTRACT
Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN) https//cran.r-project.org/web/packages/TPEA/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Perfilação da Expressão Gênica
/
Bases de Dados Genéticas
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Neoplasias
Limite:
Female
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Humans
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Male
Idioma:
En
Revista:
Brief Bioinform
Assunto da revista:
BIOLOGIA
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INFORMATICA MEDICA
Ano de publicação:
2019
Tipo de documento:
Article