TIPS: Trajectory Inference of Pathway Significance through Pseudotime Comparison for Functional Assessment of single-cell RNAseq Data
| Autor: | Shan Jiang, Xiangyu Tang, Xin Qiu, Liyun Zou, Zihan Zheng, Jianzhi Zhou, Ying Wan, Yuzhang Wu, Haiyang Wu, Jingyi Li, Ling Chang, Qingshan Ni |
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| Rok vydání: | 2020 |
| Předmět: |
Web server
Time Factors AcademicSubjects/SCI01060 Computer science Process (engineering) Cell Inference Computational biology CD8-Positive T-Lymphocytes computer.software_genre Biological pathway medicine Humans RNA-Seq Molecular Biology Gene Transcription factor Cells Cultured Internet Gene Expression Profiling Data interpretation Computational Biology Reproducibility of Results RNA Biological process Pathway analysis Visualization pathway analysis Developmental trajectory trajectory mapping medicine.anatomical_structure pseudotime Trajectory Problem Solving Protocol TIPS Single-Cell Analysis computer Information Systems Signal Transduction |
| Zdroj: | Briefings in Bioinformatics |
| DOI: | 10.1101/2020.12.17.423360 |
| Popis: | Recent advances in bioinformatics analyses have led to the development of novel tools enabling the capture and trajectory mapping of single-cell RNA sequencing (scRNAseq) data. However, there is a lack of methods to assess the contributions of biological pathways and transcription factors to an overall developmental trajectory mapped from scRNAseq data. In this manuscript, we present a simplified approach for trajectory inference of pathway significance (TIPS) that leverages existing knowledgebases of functional pathways and transcription factor targets to enable further mechanistic insights into a biological process. TIPS returns both the key pathways whose changes are associated with the process of interest, as well as the individual genes that best reflect these changes. TIPS also provides insight into the relative timing of pathway changes, as well as a suite of visualizations to enable simplified data interpretation of scRNAseq libraries generated using a wide range of techniques. The TIPS package can be run through either a web server, or downloaded as a user-friendly GUI run in R, and may serve as a useful tool to help biologists perform deeper functional analyses and visualization of their single-cell and/or large cohort RNAseq data. |
| Databáze: | OpenAIRE |
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