Gene Ontology Pathway
Gene Ontology Pathway - Related Videos
03:08
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
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2025
The current work describes a protocol for running the Pathway2Targets algorithm, an R script that predicts and prioritizes therapeutic targets based on the profile of intracellular signaling pathways generated by comparing case versus control samples from a bulk RNA-sequencing experiment.
11:42
Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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Cited by 3 •
2017
This protocol presents an approach for whole transcriptome analysis from zebrafish embryos, larvae, or sorted cells. We include isolation of RNA, pathway analysis of RNASeq data, and qRT-PCR-based validation of gene expression changes.
04:13
CRISPR Concatemer-Mediated Multiple Gene Knockout: A Technique to Simultaneously Knockout Multiple Genes by Non-Homologous End-Joining Pathway in Mouse Intestinal Cells
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2025
This video describes a gene knockout technique using a CRISPR-concatemer to simultaneously knock out multiple genes in cultured mouse intestinal organoid cells. This method is used to knock out a diseased gene and to elucidate the function of a gene and its paralogues.
02:40
Detecting SMAD Pathway Activation Using Dual Adenovirus Transduction
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2026
Source: Chen, H., et al. Live Cell Imaging of the TGF-β/Smad3 Signaling Pathway In Vitro and In Vivo Using an Adenovirus Reporter System. J. Vis. Exp. (2018).This video demonstrates a method to study SMAD pathway activation in breast cancer cells using dual adenoviral infection. One virus delivers a constitutively expressed GFP gene, while the other carries an RFP reporter under a SMAD-sensitive promoter. Upon TGF-beta stimulation, SMAD proteins are activated, forming a complex that induces RFP...
11:48
Grafting of Beads into Developing Chicken Embryo Limbs to Identify Signal Transduction Pathways Affecting Gene Expression
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Cited by 2 •
2016
By grafting beads soaked in growth factors or specific inhibitors of signaling pathways into developing embryos it is possible to directly test their effects in vivo. In this protocol beads are grafted into the limb bud to determine the effects of these molecules on gene expression and signal transduction.
FAQs
Hierarchical Gene Ontology terms let an analysis connect specific gene annotations with broader biological categories. A result can therefore be considered at several levels, from a detailed term to a larger process such as differentiation or tissue morphogenesis. This layered view helps relate individual gene observations to coordinated developmental programs.
The reference background determines what “more often than expected” means for the experimental gene set. Enrichment is assessed by comparing the observed representation of Gene Ontology terms with their representation in that background. Choosing the relevant reference is therefore essential for interpreting whether highlighted functions reflect the gene set rather than its comparison context.
The three Gene Ontology categories provide complementary perspectives on the same gene set. Biological process terms describe broader activities, molecular function terms capture what gene products do, and cellular component terms indicate where associated activity is situated within the cell. Considering all three can connect developmental events with gene-level functions and locations.
A basic workflow begins with an experimental gene set, maps its genes to hierarchical Gene Ontology terms, and then tests whether selected terms occur more frequently than expected against a reference background. The resulting enriched terms are interpreted as biological themes that summarize the gene-level observations and guide subsequent hypothesis development.
Gene Ontology Pathway analysis can be applied to transcriptomic data, genetic screens, and developmental mutants. In each case, it helps organize the affected or associated genes into functional themes rather than leaving findings as an isolated list. This supports interpretation of coordinated developmental changes across the data set.
In developmental biology, enriched terms can highlight processes such as cell differentiation, tissue morphogenesis, and signaling. These categories help researchers connect gene-level changes or mutant phenotypes with broader developmental programs. Because the results suggest relationships rather than complete explanations, they are useful for generating hypotheses that require further investigation.