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Updated: May 25, 2026
03:37
Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
Published on: March 1, 2024
Prioritizing predicted cis-regulatory elements for co-expressed gene sets based on Lasso regression models
Hong Hu1, Damian Roqueiro, Yang Dai
1Department of Bioengineering (M/C 063), University of Illinois at Chicago, 851 S Morgan St, SEO 218, Chicago, IL 60607, USA. hhu4@uic.edu
Summary
Prioritizing transcription factors for gene regulation studies is challenging. A new Lasso regression model effectively identifies key factors using gene expression data from mouse wound healing.
Area of Science:
- Genomics
- Bioinformatics
- Systems Biology
Background:
- Predicting cis-regulatory elements yields many potential transcription factor binding sites.
- Prioritizing these factors for functional studies is a significant challenge in gene regulation research.
Purpose of the Study:
- To introduce and evaluate a novel approach using Lasso regression models for prioritizing transcription factors.
- To assess the efficacy of the Lasso model in analyzing gene expression data from mouse wound healing.
Main Methods:
- Utilized Lasso regression models for computational prediction and prioritization of transcription factors.
- Analyzed time-course microarray data from mouse skin and mucosal wound healing stages.
Main Results:
- The Lasso regression model demonstrated effectiveness in prioritizing transcription factors from large datasets.
- Successfully applied the model to identify key regulatory factors during the complex process of wound healing.
Conclusions:
- Lasso regression offers a robust method for prioritizing transcription factors in regulatory genomics.
- This approach aids in focusing experimental efforts on the most relevant transcription factors for functional validation.
Related Concept Videos
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:13Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
02:13Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
02:04Co-activators and Co-repressors
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
02:04Co-activators and Co-repressors
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...