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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:36

What is Gene Expression?

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 processed and...
What is Gene Expression?01:42

What is Gene Expression?

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
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
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 24, 2026

DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data
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DeepGEP: Deep learning for gene expression prediction from multi-omics in mammals.

Jiali Cai1, Ruiqing Wang1, Yipeng Li1

  • 1State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.

Genomics
|June 22, 2026
PubMed
Summary

DeepGEP, a deep learning model, accurately predicts gene expression across species by integrating multi-omics data. It highlights key regulatory regions and histone modifications influencing gene activity.

Keywords:
Deep learningGene expression predictionMammalsMulti-omics integration

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Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • Deep neural networks show promise for multi-omics data integration.
  • Predicting gene expression and understanding regulatory mechanisms are crucial in biology.

Purpose of the Study:

  • To develop a deep learning model, DeepGEP, for predicting gene expression using multi-omics data.
  • To identify key regulatory elements and epigenetic marks involved in gene expression across species.

Main Methods:

  • Developed DeepGEP, an attention-based Long Short-Term Memory model.
  • Trained on 228 datasets including RNA-seq, ATAC-seq, and ChIP-seq (H3K4me3, H3K4me1, H3K27ac, H3K27me3) from humans, pigs, and cattle.
  • Analyzed attention weights to identify important genomic regions and histone modifications.

Main Results:

  • DeepGEP achieved high prediction accuracy (PCC 0.70-0.82, up to 0.93 with clustering).
  • Attention analysis identified regulatory regions near transcription start sites.
  • H3K4me3 and chromatin accessibility were the strongest predictors of gene expression.

Conclusions:

  • Integrating chromatin accessibility and histone modifications enables accurate cross-species gene expression prediction.
  • DeepGEP provides a versatile framework for multi-omics modeling.
  • The study advances the understanding of mammalian gene regulation.