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Related Concept Videos

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...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Updated: May 18, 2026

Development of Compendium for Esophageal Squamous Cell Carcinoma
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Published on: April 12, 2024

The GENCODE pseudogene resource.

Baikang Pei1, Cristina Sisu, Adam Frankish

  • 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Genome Biology
|September 7, 2012
PubMed
Summary
This summary is machine-generated.

Pseudogenes, once thought nonfunctional, are now recognized for potential biological activity. This study provides a genome-wide annotation and functional analysis, revealing pseudogenes with varying activity levels, some possibly acting as non-coding RNAs.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Pseudogenes were historically considered nonfunctional genomic relics.
  • Emerging evidence suggests pseudogenes may possess biological activity and regulatory roles.
  • Accurate pseudogene annotation is crucial for integrating functional genomics data.

Purpose of the Study:

  • To perform the first genome-wide pseudogene assignment for protein-coding genes.
  • To integrate pseudogene annotations with functional genomics data from ENCODE.
  • To identify pseudogenes with potential biological activity and evolutionary selection.

Main Methods:

  • Combined large-scale manual annotation and in silico pipelines for pseudogene identification.
  • Integrated pseudogene data with ENCODE functional genomics information (expression, transcription factor binding, chromatin marks).
  • Developed statistical models for pseudogene activity, validated by RT-PCR-Seq, and compared with conservation and variation data.

Main Results:

  • Presented a comprehensive genome-wide pseudogene assignment using a coupled annotation approach.
  • Characterized pseudogene activity, including expression levels, transcription factor binding, and chromatin marks.
  • Identified pseudogenes potentially under selection by comparing with primate and human variation data.

Conclusions:

  • Some pseudogenes exhibit characteristics of recent gene death and potential functionality.
  • Observed patterns suggest pseudogenes can be repurposed as functional non-coding RNAs.
  • The psiDR resource facilitates the identification of potentially functional pseudogenes.