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Related Concept Videos

Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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Mutation, Gene Flow, and Genetic Drift01:09

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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Spontaneous and Induced Mutations01:30

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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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Updated: Aug 7, 2025

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
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Influence network model uncovers relations between biological processes and mutational signatures.

Bayarbaatar Amgalan1, Damian Wojtowicz1,2, Yoo-Ah Kim1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA.

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|March 6, 2023
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GENESIGNET reveals connections between mutational signatures and gene expression. This network approach helps understand cancer processes by linking mutation patterns to cellular pathways.

Keywords:
APOBECBreast cancerCausality inferenceMutational processes in cancerMutational signaturesNetworks

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Mutational signatures offer insights into mutagenic processes.
  • Understanding the links between mutagens, mutation patterns, and molecular pathways is crucial but incomplete.

Purpose of the Study:

  • To develop a network-based method for uncovering relationships between genes and mutational signatures.
  • To enhance the utility of mutational signatures in understanding biological processes.

Main Methods:

  • Developed GENESIGNET, a network-based approach.
  • Utilized sparse partial correlation to identify influence relations between network nodes (genes and mutational signatures).

Main Results:

  • Uncovered significant relationships between mutational signatures and cellular processes in cancer data.
  • Confirmed known interactions, such as homologous recombination deficiency and APOBEC mutations.
  • Identified novel potential links between APOBEC hypermutation and regulatory T Cells (Tregs), DNA conformation changes, and the Nucleotide Excision Repair (NER) pathway with the SBS8 signature.

Conclusions:

  • GENESIGNET offers a powerful new method for exploring connections between mutational signatures and gene expression.
  • The tool facilitates deeper understanding of cancer-related biological processes.