Questions tagged [gene-ontology]
The Gene Ontology (GO) is a collection of annotations of genes from multiple species to terms describing the functional role of those genes. The terms are organized in a graph structure that allows for propagation of information. See http://geneontology.org
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How can I create my own GO slim?
I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?
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Bonferroni count = 1 in GO-Slim overrepresentation test (PANTHER) is it possible?
I encountered a problem while performing analysis using the PANTHER website. I run the statistical overrepresentation test for a genelist of 99 genes (GO-Slim BP, Binomial, Bonferroni) in February ...
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Gene Ontology equivalent - higher specificity?
I've recently discovered OrthoVenn2, which I'm using to compare proteomes and extract likely clade-specific genes. I'm enjoying software, and one of the things it offers is a breakdown of protein ...
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Gene Ontology Specific Fold Changes
I am currently doing a project involving gene rank correlations. How we rank our genes is based on the absolute values of the log2 fold change. I.e. a gene which is doubled with respect to the ...
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Gene Ontology (GO) analysis and classification of bacterial whole genome annotations
I am new to Gene Ontology (GO) analysis and would like to classify and visualize the annotations. Here is the background and the steps I have taken so far:
I annotated the bacterial whole genome ...
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How to identify specific motif for chip-seq data
For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
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