scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures

Abstract

The most fundamental challenge in current single-cell RNA-seq data analysis is functional interpretation and annotation of cell clusters. The biological pathways in distinct cell types have different activation patterns, which facilitates understanding cell functions in single-cell transcriptomics. However, no effective web tool has been implemented for single-cell transcriptomic data analysis based on prior biological pathway knowledge. Here, we introduce scTPA (http://sctpa.bio-data.cn/sctpa), which is a web-based platform providing pathway-based analysis of single-cell RNA-seq data in human and mouse. scTPA incorporates four widely-used gene set enrichment methods to estimate the pathway activation scores of single cells based on a collection of available biological pathways with different functional and taxonomic classifications. The clustering analysis and cell-type-specific activation pathway identification were provided for the functional interpretation of cell types from pathway-oriented perspective. An intuitive interface allows users to conveniently visualize and download single-cell pathway signatures. Together, scTPA is a comprehensive tool to identify pathway activation signatures for dissecting single cell heterogeneity.

PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology

“…To compute and analyze pathway scores in malignant cholangiocarcinoma cells, we used scTPA, which is a web tool for single-cell analysis of activated pathways ( ) ( 27 , 28 ). The malignant cell expression matrix was extracted by sample origins in malignancy and cholangiocyte cluster, and then expression matrix was uploaded online.…”