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Related Concept Videos

Structure of a Gene01:30

Structure of a Gene

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A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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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...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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What is Gene Expression?01:36

What is Gene Expression?

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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What is Gene Expression?01:42

What is Gene Expression?

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Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
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Updated: Nov 7, 2025

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
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Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

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Protein structure-based gene expression signatures.

Rayees Rahman1, Nicole Zatorski2, Jens Hansen2,3

  • 1Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029; rayees.rahman@icahn.mssm.edu ravi.iyengar@mssm.edu avner.schlessinger@mssm.edu.

Proceedings of the National Academy of Sciences of the United States of America
|May 4, 2021
PubMed
Summary
This summary is machine-generated.

Structural gene expression signatures (sGES) improve gene set analysis by incorporating protein structure. This approach enhances reproducibility and biological characterization across diverse datasets and experimental platforms.

Keywords:
gene expression signaturesreproducibilitystructural bioinformatics

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Gene expression signatures (GES) link phenotypes to messenger RNA (mRNA) expression, aiding cellular identity and function definition.
  • Current GES methods face challenges with vague assessment criteria and limited reproducibility.
  • Protein structure dictates gene function, suggesting structural features as a basis for improved gene set representation.

Purpose of the Study:

  • To develop and validate structural gene expression signatures (sGES) by integrating protein structural features into gene sets.
  • To enhance the generalizability, reproducibility, and biological interpretability of gene expression signature analysis.
  • To demonstrate the utility of sGES in characterizing biological phenomena across different datasets and experimental contexts.

Main Methods:

  • Derived sGES by encoding mRNA-derived protein structural features (domains, folds) from existing gene sets.
  • Analyzed sGES using data from the Genotype-Tissue Expression Project (GTEx) and the ARCHS4 database.
  • Evaluated sGES performance in characterizing drug effects on cardiomyocyte mRNA expression.

Main Results:

  • sGES provide a robust and generalizable representation of gene sets by incorporating protein structural information.
  • Demonstrated the utility of sGES for characterizing biological phenomena across diverse datasets, including GTEx and ARCHS4.
  • sGES effectively describe drug actions on cells and enable phenotypic characterization across experimental platforms.

Conclusions:

  • sGES offer a significant advancement over traditional GES by leveraging protein structure for enhanced biological insight.
  • sGES facilitate improved interoperability between different gene expression datasets.
  • The sGES approach holds promise for more accurate and reproducible biological characterization and drug effect analysis.