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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Master Transcription Regulators02:23

Master Transcription Regulators

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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...
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Regulation of Expression Occurs at Multiple Steps02:24

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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Co-activators and Co-repressors02:04

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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...
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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Related Experiment Video

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Functional Enrichment Analysis of Regulatory Elements.

Adrian Garcia-Moreno1, Raul López-Domínguez1,2, Juan Antonio Villatoro-García1,2

  • 1Bioinformatics Unit, Centre for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain.

Biomedicines
|March 25, 2022
PubMed
Summary
This summary is machine-generated.

New statistical methods enhance enrichment analysis for regulatory elements like CpG sites and miRNAs. These tools, available in GeneCodis 4, improve biological information extraction from omics data.

Keywords:
enrichment analysisfunctional analysisgene set analysisregulationweb tool

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Omics experiments generate vast datasets requiring robust statistical analysis.
  • Existing enrichment analysis tools primarily focus on gene and protein lists.
  • High-throughput technologies for regulatory elements necessitate specialized bioinformatics tools.

Purpose of the Study:

  • To develop novel statistical and bioinformatics methods for enrichment analysis of regulatory elements.
  • To address the limitations of current tools in analyzing CpG sites, miRNAs, and transcription factors.
  • To provide a web tool for singular and modular enrichment analysis integrating heterogeneous information.

Main Methods:

  • Developed a set of enrichment analysis methods for regulatory elements.
  • Utilized a power weighting function for target genes to determine statistical significance.
  • Employed the Wallenius noncentral hypergeometric distribution model to mitigate selection bias.
  • Integrated these methods into the GeneCodis 4 web tool.

Main Results:

  • Successfully applied the new methodologies to analyze miRNAs associated with arrhythmia.
  • Demonstrated the potential of the developed tool to extract meaningful biological insights from regulatory element lists.
  • GeneCodis 4 offers singular and modular enrichment analysis capabilities.

Conclusions:

  • The new enrichment analysis methods provide a powerful approach for dissecting regulatory element data in omics studies.
  • GeneCodis 4 facilitates the integration of diverse biological information for comprehensive analysis.
  • These advancements are crucial for advancing our understanding of regulatory element functions in biological processes.