WebCSEA: web-based cell-type-specific enrichment analysis of genes. Issue Volume 50:Issue W1(2022) (24th May 2022)

• Record Type: Journal Article
• Authors: Dai, Yulin; Hu, Ruifeng; Liu, Andi; Cho, Kyung Serk; Manuel, Astrid Marilyn; Li, Xiaoyang; Dong, Xianjun; Jia, Peilin; Zhao, Zhongming
• Is Part Of: Nucleic acids research. Volume 50:Issue W1(2022)
• Page Start: W782
• Page End: W790
• Publication Date: 2022-05-24
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac392
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Human complex traits and common diseases show tissue- and cell-type- specificity. Recently, single-cell RNA sequencing (scRNA-seq) technology has successfully depicted cellular heterogeneity in human tissue, providing an unprecedented opportunity to understand the context-specific expression of complex trait-associated genes in human tissue-cell types (TCs). Here, we present the first web-based application to quickly assess the cell-type-specificity of genes, named Web-based Cell-type Specific Enrichment Analysis of Genes (WebCSEA, available at https://bioinfo.uth.edu/webcsea/ ). Specifically, we curated a total of 111 scRNA-seq panels of human tissues and 1, 355 TCs from 61 different general tissues across 11 human organ systems. We adapted our previous decoding tissue-specificity ( deTS ) algorithm to measure the enrichment for each tissue-cell type (TC). To overcome the potential bias from the number of signature genes between different TCs, we further developed a permutation-based method that accurately estimates the TC-specificity of a given inquiry gene list. WebCSEA also provides an interactive heatmap that displays the cell-type specificity across 1355 human TCs, and other interactive and static visualizations of cell-type specificity by human organ system, developmental stage, and top-ranked tissues and cell types. In short, WebCSEA is a one-click application that provides a comprehensive exploration of the TC-specificity of genes among human major TC map. Graphical Abstract: