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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
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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...
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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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Pattern-based Search of Epigenomic Data Using GeNemo
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Multidimensional gene search with Genehopper.

Matthias Munz1, Sascha Tönnies1, Wolf-Tilo Balke1

  • 1Institute for Information Systems, Technische Universität Braunschweig, Braunschweig 38106, Germany.

Nucleic Acids Research
|May 21, 2015
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Summary
This summary is machine-generated.

Genehopper is a new search engine that allows researchers to explore gene-to-gene relationships using multidimensional scoring. It enables flexible customization of gene similarity searches for deeper biological insights.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput sequencing generates vast genetic information, necessitating advanced tools for comparative analysis.
  • Existing gene exploration tools often analyze similarity metrics independently, limiting comprehensive relationship discovery.

Purpose of the Study:

  • To develop a novel search engine, Genehopper, for exploring multidimensional gene-to-gene relationships.
  • To enable flexible and customizable gene similarity searches by integrating multiple data dimensions.

Main Methods:

  • Implemented a web-based search engine, Genehopper, supporting term-to-gene and gene-to-gene queries.
  • Integrated nine normalized gene similarity metrics (e.g., homology, expression, ontology) into a weighted sum model.
  • Allowed user-adjustable weights for each similarity dimension to customize search rankings.

Main Results:

  • Genehopper facilitates exploration of gene neighborhoods based on a user-defined combination of similarity metrics.
  • The low pairwise correlation between similarity metrics ensures that user weight adjustments significantly impact gene ranking.
  • The search engine supports various gene identifiers (Ensembl, UniProt, EntrezGene, RefSeq) and terms.

Conclusions:

  • Genehopper provides a powerful and flexible platform for uncovering complex gene-to-gene relationships.
  • The multidimensional scoring approach enhances the discovery of novel biological insights from genetic data.
  • The tool is freely available, promoting wider adoption in biological research.