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Related Concept Videos

Gene Families01:57

Gene Families

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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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Protein Families02:47

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Gene Duplication and Divergence02:37

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
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WHEN SHOULD WE NOT TRANSFER FUNCTIONAL ANNOTATION BETWEEN SEQUENCE PARALOGS?

Mengfei Cao1, Lenore J Cowen

  • 1Department of Computer Science, Tufts University, Medford, MA 02155, USA, mengfei.cao@tufts.edu.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|November 30, 2016
PubMed
Summary
This summary is machine-generated.

Determining when to transfer gene function between paralogs is crucial. This study finds sequence divergence is a key indicator, suggesting caution when divergence is high for accurate functional annotation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Automated gene function assignment often relies on transferring annotations between homologous genes (orthologs or paralogs).
  • Paralogous genes can evolve distinct functions, making direct annotation transfer potentially inaccurate.
  • Assessing the reliability of functional annotation transfer between paralogs is essential for accurate gene function prediction.

Purpose of the Study:

  • To investigate the feasibility of predicting functional similarity/divergence between paralogous genes using single-species data.
  • To identify features from sequence and protein-protein interaction network data that can distinguish between functionally similar and divergent paralogs.
  • To establish criteria for appropriate functional annotation transfer between paralogs within a single species.

Main Methods:

  • Construction of a benchmark dataset of paralogous gene pairs in *S. cerevisiae* with known similar or divergent phenotypes.
  • Analysis of sequence divergence (amino acid and nucleotide levels) between paralogs.
  • Exploration of protein-protein interaction (PPI) network features, including degree, centrality, shortest path, and diffusion state distance (DSD).
  • Evaluation of the predictive power of these features for distinguishing functional similarity.

Main Results:

  • Sequence divergence measures were found to be the most effective features for distinguishing between functionally similar and divergent paralogs.
  • Protein-protein interaction network features, such as degree, centrality, and shared neighborhood, also provided some predictive signal.
  • A high degree of sequence divergence generally indicates that functional transfer should not be performed.

Conclusions:

  • Single-species data, particularly sequence divergence, can offer valuable insights into the functional relatedness of paralogous genes.
  • While PPI network data contributes, sequence divergence appears to be a more robust predictor within a single species.
  • Future advancements in accurately transferring gene function will likely require multi-species evolutionary analyses incorporating ancestral states.