1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Demonstration of cellular dynamic behavior in response to DNA damage through gene regulatory network analysis of single-cell resolution ‌DNA repair phenotype and gene expression multi-omics dataset
Paper ID : 1207-ICB10
Authors:
Abolfazl Arab *1, Sama Goliaei1, Faramarz Mehrnejad2
1Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
2Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
Abstract:
A lot of genes may involve in the response of cells to DNA damage occurrence and regulation of these genes are complicated at different levels [1]–[3]. Also, it is known that their missing activity has important roles in cancer diseases and treatment [4], [5]. Droplet microfluidics and Next Generation Sequencing (NGS) are enabling technologies to evaluate genomic complexity in single-cell resolution [6]. In general, these methods extract a large amount of data from different layers of biological information which opens computational challenges to analyze these big data toward biological interpretations [7]. Richer et. al, 2020, used nano-biomimetic substrates containing arbitrary lesion DNA damage to quantitatively evaluate the relationship of gene expression and repair phenotype in single-cell resolution [8]. Among their data, we have selected time-series experiments on the HAP1 cancer cell line and designed our analysis workflows to reanalyze the available multi-omics data. Basically, for each cell, we have both gene expression profile and DNA repair measurement simultaneously. We used statistical inference, mathematical modeling, and graph analysis of context-specific gene regulatory networks (GRN) to mine this data [9]–[11]. Also, we are connecting our data with publicly available datasets such as protein-protein interaction (PPI) [12] and molecular signature database (MSigDB) [13].
Keywords:
Single-cell; RNA expression; RNA-seq; Omics; Multi-omics; Enzyme activity; DNA Damage; DNA Repair; Gene Regulatory Network; Gene-set analysis; Network analysis
Status : Paper Accepted (Poster Presentation)