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Identification and comparison of genes differentially regulated by transcription factors and miRNAs

Amir Asiaee, Zachary B Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
doi: https://doi.org/10.1101/803643
Amir Asiaee
1Mathematical Biosciences Institute, The Ohio State University, Columbus, 43210, USA
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  • For correspondence: zachary.abrams@osumc.edu
Zachary B Abrams
2Department of Biomedical Informatics, The Ohio State University, Columbus, 43210, USA
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  • For correspondence: zachary.abrams@osumc.edu
Samantha Nakayiza
2Department of Biomedical Informatics, The Ohio State University, Columbus, 43210, USA
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Deepa Sampath
3Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, 43210, USA
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Kevin R. Coombes
2Department of Biomedical Informatics, The Ohio State University, Columbus, 43210, USA
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Abstract

Transcription factors and microRNAs (miRNA) both play a critical role in gene regulation and in the development of many diseases such as cancer. Understanding how transcription factors and miRNAs influence gene expression is thus important to understand, but complicated due to the large and interconnected nature of the human genome. To help better understand what genes are being regulated by transcription factors and/or miRNAs we looked at it over 8000 patient samples from 32 different cancer types collected from The Cancer Genome Atlas (TCGA). We started by clustering the transcription factors and miRNAs using Thresher to reduce the number of features. Using both the mRNA and miRNA sequencing data we constructed linear models to calculate the coefficient of determination (R2) for each mRNA based on the Thresher cluster expression. We generated three types of linear models: transcription factor, miRNA and transcription factor plus miRNA. We then determined genes that were highly explained or poorly explained by each of the three models based on the genes R2 value. We performed downstream gene enrichment analysis using ToppGene on the sets of well and poorly explained genes. This identified differences in gene regulation between transcription factors and miRNAs and showed what groups of gene are differentially regulated.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 13, 2019.
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Identification and comparison of genes differentially regulated by transcription factors and miRNAs
Amir Asiaee, Zachary B Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
bioRxiv 803643; doi: https://doi.org/10.1101/803643
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Identification and comparison of genes differentially regulated by transcription factors and miRNAs
Amir Asiaee, Zachary B Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
bioRxiv 803643; doi: https://doi.org/10.1101/803643

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