CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters.
Brief Bioinform
; 25(2)2024 Jan 22.
Article
em En
| MEDLINE
| ID: mdl-38279653
ABSTRACT
Cluster analysis is one of the most widely used exploratory methods for visualization and grouping of gene expression patterns across multiple samples or treatment groups. Although several existing online tools can annotate clusters with functional terms, there is no all-in-one webserver to effectively prioritize genes/clusters using gene essentiality as well as congruency of mRNA-protein expression. Hence, we developed CAP-RNAseq that makes possible (1) upload and clustering of bulk RNA-seq data followed by identification, annotation and network visualization of all or selected clusters; and (2) prioritization using DepMap gene essentiality and/or dependency scores as well as the degree of correlation between mRNA and protein levels of genes within an expression cluster. In addition, CAP-RNAseq has an integrated primer design tool for the prioritized genes. Herein, we showed using comparisons with the existing tools and multiple case studies that CAP-RNAseq can uniquely aid in the discovery of co-expression clusters enriched with essential genes and prioritization of novel biomarker genes that exhibit high correlations between their mRNA and protein expression levels. CAP-RNAseq is applicable to RNA-seq data from different contexts including cancer and available at http//konulabapps.bilkent.edu.tr3838/CAPRNAseq/ and the docker image is downloadable from https//hub.docker.com/r/konulab/caprnaseq.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Proteômica
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Brief Bioinform
Ano de publicação:
2024
Tipo de documento:
Article