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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-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...
Cis-regulatory Sequences02:02

Cis-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...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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 addition of a...

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Related Experiment Video

Updated: Jun 12, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
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Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple

Atsushi Niida1, Seiya Imoto, Rui Yamaguchi

  • 1Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan. aniida@ims.u-tokyo.ac.jp

Plos One
|June 15, 2010
PubMed
Summary

We developed BEEM (Biclustering-based Extraction of Expression Modules), a novel computational method to identify gene expression modules specific to subsets of human tissues. BEEM uncovers crucial regulatory programs missed by existing approaches, enhancing our understanding of transcriptomic diversity.

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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
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Published on: July 29, 2022

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Decoding transcriptional programs across human tissues is complex.
  • Existing methods for cis-regulatory code analysis have limitations in identifying tissue-subset-specific expression modules.
  • Current approaches based on differential expression or expression coherence struggle with multi-tissue datasets.

Purpose of the Study:

  • To develop a novel computational method for discovering expression modules functional in a subset of tissues.
  • To overcome the limitations of existing methods in capturing tissue-specific transcriptional programs.
  • To gain new insights into the regulatory mechanisms driving transcriptomic diversity across human tissues.

Main Methods:

  • Developed BEEM (Biclustering-based Extraction of Expression Modules), a new module discovery method.
  • Applied BEEM to human multiple tissue expression profiles.
  • Compared BEEM's performance against existing methods based on coherent expression and single tissue-specific differential expression.

Main Results:

  • BEEM successfully identified expression modules missed by existing approaches.
  • The method revealed novel insights into transcriptional programs governing transcriptomic diversity.
  • BEEM demonstrated superior performance in discovering tissue-subset-specific expression modules.

Conclusions:

  • BEEM is a powerful tool for decoding regulatory programs from gene expression data.
  • The developed method enhances the analysis of transcriptomic diversity across multiple human tissues.
  • BEEM facilitates a deeper understanding of the cis-regulatory codes underlying tissue-specific gene expression.