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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Retrieve gene symbols of genes from GO term with Python

Is there a way to retrieve the gene symbols belonging to a GO term with Python ? For example, the GO:0006096 (glycolytic process) contains 96 genes: ...
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How do I get GO annotations for a list of UniProt IDs?

I have a list of UniProt ids that I want to get Gene Ontology annotations for. I need this information because I want this high-level information as an input to a neural network. The model I wish to ...
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RDAVIDWebService (R package) manual installation, or alternative tool

Recently, I had to re-install all my R packages (R version 4.1.0 (2021-05-18) -- "Camp Pontanezen") and it turns out that "RDAVIDWebService" is ...
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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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Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
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How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
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gprofiler output ENSG to gene name

I would like to ask if there is any tool or R script that translates Ensembl IDs to gene names in a gprofiler GO output. An example of this file is the following one:
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Parsing the json file from gene ontology result into dataframe

How do I parse the json file from ontology output. My file json file jdata <- read_json("analysis.json", simplifyVector = TRUE) I want to convert it ...
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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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Analyzing proteins based on sequence similarity

Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic ...
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How to identify latent variables in single-cell RNA-Seq data

I have a single-cell RNASeq sample, in which I'd like to identify latent variables (e.g. response to stress) that I think might be affecting the clustering. The approach I was planning to use is to ...
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Interpreting a kernel density function plot of gene expression

I need help interpreting a kernal density plot and a histogram of this data. I have provided some context below let me know if you need more information A co-worker that I am collaborating with has a ...
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Why are my genes filtered for Gene Ontology term enrichment?

When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment: I am struggling to ...
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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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Discordance of Gene Ontology data between Mouse Genome Informatics and Ensembl sources

In my first approach to the use of Gene Ontology, I have found a discordance if we consult either Mouse Genome Informatics (MGI) or Ensembl for these data. Concretely, for the mouse genes Zic1 (NCBI ...
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How do i map subcellular localizations to lower the number of classes to predict

For a project, I want to predict the subcellular localization of some proteins. I am a student in software Informatics at the University of applied Science HEIG-VD. Subcellular localization ...
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How do I perform a pathway related grouping of genes?

I have a list of gene names from the analysis of my mouse single seq data. I want to perform a simple grouping of the genes based on the pathways to which they belong or pathways through which they ...
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different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
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Retrieve all genes for a specific gene ontology

I'm having a bit of confusion about how can I retrieve all the genes that are associated to a specific gene ontology. Lets say I need to find all the genes that are associated with this GO entry: ...
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NCBI xml-format Printing nodeValues from tags with the same names

I would like to retrieve all Other-source_anchor on the level of DNA binding from within a Gene Ontology XML file using php. If I try this with my code, I only get Gene Ontology back and not the ...
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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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Obtain CD (cluster of differentiation) marker expression information

There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
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Retrieving a list of human genes having GO associations

I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.
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How can I create my own GO association file (gaf)?

This question is based on a question on BioStars posted >2 years ago by user jack. It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on ...
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