Questions tagged [go-enrichment]

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How to get the GO information for all the human genes?

I would like to find a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific enough, ...
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20 views

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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2answers
36 views

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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1answer
24 views

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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3answers
47 views

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: ...
1
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1answer
36 views

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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2answers
96 views

Alternative to enrichR for enrichment analysis?

I have been using EdgeR 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, ranked by the their adjP ...
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0answers
72 views

Question about enrichment score (ES) and NES from GSEA

I have two results from separated two GSEA runs, and i want to know which sample has the most enrichment about specific pathway (gene set). Can I use ES (or NES) from two different GSEA analysis ...
4
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1answer
141 views

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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0answers
125 views

How can I calculate and compare intra-cluster correlation for each GO term and pathway?

How can I calculate and compare intra-cluster correlation for each GO term and pathway? I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...
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2answers
51 views

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 ...
5
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2answers
143 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 ...
4
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2answers
444 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 ...