Questions tagged [go-enrichment]

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What genes are driving a certain pathway

I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway. ...
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Does it make sense to perform pathway enrichment analysis on a list of mutated genes from a VCF?

I have a list of mutated genes from a VCF. Does it make sense to perform a pathway enrichment analysis using PANTHER or STRING as examples to know which pathway is affected? EDIT: to reply to @terdon ...
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How to Interpret Author's Methods in this article?

I have to reproduce a result for school reasons (bioinformatics exam) and I was assigned a certain article. In particular I have to reproduce what some authors did in: doi: 10.1371 / journal.pone....
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Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
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What type of Protein ID is this?

I got a FASTA file from NCBI RefSeq. These proteins are annotated with IDs like this : protein_id=XP_019970915.1. What type of ID is this? I would like to have them converted in TrEMBL IDs in order to ...
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is it ok to use gene sets from an organism to enrich genes from a different organism?

Lets say I performed a single cell RNA sequencing analysis on mice blood samples. Eventually I am able to cluster cells together and get a set of genes of interest for each cell type since I want to ...
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less than 80% of your list has mapped to your chosen identifier type

I am trying to do GO analysis. However, when I run DAVID, I am getting this error: You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your ...
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Pathway enrichment analysis with or without custom background

I am doing a pathway enrichment analysis of a sets of proteins. Specific cell types (cardiospheres) were used to perform the experiment and for the quantification of proteins was used mass ...
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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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are GSEA and other geneset enrichment analysis supposed to yield extremely different results between them?

I have recently ran in R four geneset enrichment analysis in the same database (TCGA:breast cancer) comparing two intrinsic subtypes. The methods I used were: MIGSA, that imports mGSZ package and ...
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How to get the GO information for all the human genes?

I would like to retrieve a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific ...
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How to detail the specific GO terms

How can I get more specific GO terms when using clusterProfiler? I got my Dotplot by: ...
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about GO terms's name

Did anyone know whether the GO terms can include more detail information? Like I can get the DotPlot of the GO terms as below: The problem is that some of the genes, in the GO terms, is more about ...
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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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3 answers
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How to convert a list of genes to one element per row?

I got two lists of about 300 genes from my GO analysis, like the following: ...
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1 answer
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Compare functional enrichment between genelists

I want to compare the results from functional enrichment (e.g GO term enrichment generated by gProfileR) between two gene lists. The idea is to see if these gene lists are enriched in the same terms ...
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Alternative to enrichR for enrichment analysis?

I have been using EdgeR from the Bioconductor package to perform differential expression analysis on bulk RNASeq data sets. This analysis gives me an output dataframe that has a list of all the genes, ...
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Question about enrichment score (ES) and NES from GSEA

I have two results from two separate GSEA runs (2 different inputs / samples with same gene sets), and i want to know which sample has the most enrichment about specific pathway (gene set). I want to ...
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GOseq analysis with evidence code filter

When using GOseq analysis on RNA-seq data, I often find many 'false positives'. What I mean with that is that some genes in certain categories are not really involved in the process, but are only ...
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Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

As the question states, I am interested in an analysis similar to Gene Set Enrichment Analysis (ranked gene sets) but focused on locus-level data instead of genes. To explain in greater detail: I ...
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6 votes
2 answers
222 views

Clarification on Gene Enrichment

When I run a GSEA analysis on two conditions from the same RNaseq (negative control PBS injection VS positive control CpG injection) from the same dataset/same gene list, I get results that look ...
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5 votes
2 answers
779 views

How to run enrichment analysis of protein functional annotation?

I have a lot of protein clusters. I want to perform an enrichment analysis of their functional annotations, against reference datasets or list of genes I select. More precisely: a method yields ...
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