HGCA2.0: An RNA-Seq Based Webtool for Gene Coexpression Analysis in Homo sapiens.
Cells
; 12(3)2023 01 21.
Article
in English
| MEDLINE | ID: covidwho-2289161
ABSTRACT
Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Gene Expression Profiling
/
Gene Regulatory Networks
/
Genes
Type of study:
Prognostic study
Limits:
Humans
Language:
English
Year:
2023
Document Type:
Article
Affiliation country:
Cells12030388
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