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Related Concept Videos

In-vitro Mutagenesis01:16

In-vitro Mutagenesis

To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
Genetic Screens02:46

Genetic Screens

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 result in visible changes...
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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Related Experiment Video

Updated: Jun 28, 2026

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells
11:35

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells

Published on: June 16, 2017

Information-based methods for predicting gene function from systematic gene knock-downs.

Matthew T Weirauch1, Christopher K Wong, Alexandra B Byrne

  • 1Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. weirauch@soe.ucsc.edu

BMC Bioinformatics
|October 31, 2008
PubMed
Summary
This summary is machine-generated.

Information-based metrics improve gene function prediction by analyzing phenotypic knock-down profiles. This approach effectively identifies novel gene modules with shared biological roles, enhancing functional genomics insights.

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Last Updated: Jun 28, 2026

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells
11:35

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells

Published on: June 16, 2017

Combining Optogenetics with Artificial microRNAs to Characterize the Effects of Gene Knockdown on Presynaptic Function within Intact Neuronal Circuits
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Combining Optogenetics with Artificial microRNAs to Characterize the Effects of Gene Knockdown on Presynaptic Function within Intact Neuronal Circuits

Published on: March 14, 2018

Pooled CRISPR-Based Genetic Screens in Mammalian Cells
09:05

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

Area of Science:

  • Genomics
  • Functional Genomics
  • Systems Biology

Background:

  • High-throughput RNA interference assays enable genome-wide gene annotation.
  • Numerous RNA interference phenotypes have been cataloged for Caenorhabditis elegans.
  • Effective utilization of knock-down phenotypes for gene function prediction remains an open question.

Purpose of the Study:

  • To compare methods for detecting gene-gene functional similarity from phenotypic knock-down profiles.
  • To identify optimal strategies for leveraging phenotypic data in functional genomics.
  • To discover novel gene modules with shared biological functions.

Main Methods:

  • Comparison of information-based and non-information-based similarity measures.
  • Analysis of phenotypic knock-down profiles in Caenorhabditis elegans.
  • Construction of an integrated functional network using phenotypic congruency links.

Main Results:

  • Information-based measures significantly outperform non-information-based methods in detecting gene-gene functional similarity.
  • Newly predicted gene modules were identified using an integrated functional network.
  • A novel module of genes involved in regulating body morphology was discovered, linked to the TGF-beta signaling pathway.

Conclusions:

  • Information-based metrics enhance the comparison of phenotypic knock-down profiles.
  • These metrics improve gene function prediction accuracy.
  • Novel functional gene modules can be effectively identified using this approach.