CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters

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...

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Bibliographic Details
Published in:Briefings in bioinformatics 2024-01, Vol.25 (2)
Main Authors: Vural-Ozdeniz, Merve, Calisir, Kubra, Acar, Rana, Yavuz, Aysenur, Ozgur, Mustafa M, Dalgıc, Ertugrul, Konu, Ozlen
Format: Article
Language:English
Subjects:
Annotations
Biomarkers
Cluster analysis
Clustering
Gene expression
Genes
Protein expression
Proteins
Proteomics
Ribonucleic acid
RNA
RNA, Messenger - genetics
RNA-Seq
Sequence Analysis, RNA - methods
Visualization
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Summary: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.tr:3838/CAPRNAseq/ and the docker image is downloadable from https://hub.docker.com/r/konulab/caprnaseq.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbad536