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Related Concept Videos

Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

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).
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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...
Mutations in Microorganisms01:18

Mutations in Microorganisms

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,...
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Mutations01:39

Mutations

Overview

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Towards linked open gene mutations data.

Achille Zappa1, Andrea Splendiani, Paolo Romano

  • 1Bioinformatics, IRCCS AOU San Martino-IST National Cancer Research Institute, Genoa, I-16132, Italy.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

This study integrates the IARC TP53 Mutation database into Linked Open Data, enabling new ways to query gene variation data. This advance supports personalized medicine through enhanced data retrieval and reasoning on biological databases.

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Area of Science:

  • Bioinformatics
  • Genomics
  • Semantic Web technologies

Background:

  • High-throughput technologies generate vast amounts of genetic variation data, crucial for genotype-phenotype correlations and personalized medicine.
  • Existing gene variation databases lack comprehensive integration within the Semantic Web framework.
  • The Semantic Web offers a powerful infrastructure for linking and querying diverse biological datasets.

Purpose of the Study:

  • To address the scarcity of gene variation data in the Semantic Web.
  • To develop a method for integrating the IARC TP53 Mutation database into Linked Open Data.
  • To enable new forms of data retrieval and analysis for mutation data.

Main Methods:

  • Utilized a relational database version of the IARC TP53 Mutation database.
  • Employed D2RQ for automatic mapping to Resource Description Framework (RDF).
  • Manually refined mappings using domain vocabularies and ontologies, linking to existing Linked Open Data resources.
  • Loaded RDF data into a Jena-based system for improved query performance.

Main Results:

  • Developed and implemented a D2RQ Server for TP53 mutation data, including gene variations, somatic mutations, and references.
  • Enabled browsing of the RDF graph with inter-class and external system links.
  • Provided an alternative interface with enhanced performance for SPARQL queries.
  • Made mutation data explorable via standard Semantic Web browsers and applications.

Conclusions:

  • Successfully exposed a mutation database as Linked Data for the first time.
  • Ongoing development of a revised prototype with expanded datasets and concepts.
  • Publication of variation data as Linked Data opens new avenues for data retrieval and analysis.
  • Integration and reasoning on variation data hold potential for advancing personalized medicine.