PT  - JOURNAL ARTICLE
AU  - Xiaojun Ma
AU  - Ashwin Somasundaram
AU  - Zengbiao Qi
AU  - Harinder Singh
AU  - Hatice Ulku Osmanbeyoglu
TI  - SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators
AID  - 10.1101/2020.12.22.423961
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.12.22.423961
4099  - http://biorxiv.org/content/early/2020/12/22/2020.12.22.423961.short
4100  - http://biorxiv.org/content/early/2020/12/22/2020.12.22.423961.full
AB  - The developmental pathways and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to peripheral blood mononuclear cells (PBMCs) to predict the coupling of signaling receptors with cell context-specific TF activities. The predictions are validated by flow cytometry analyses. SPaRTAN is then used to analyze the signaling coupled TF activity states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN greatly enhances the utility of CITE-seq datasets to probe signaling coupled TF networks that regulate developmental or functional transitions in cellular states.Competing Interest StatementThe authors have declared no competing interest.