Questions tagged [go-enrichment]

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For gene enrichment analysis, what are the difference among ORA, globaltest, and GSVA?

I am still new to bioinformatics, but I would like to know more about the algorithms for gene enrichment analysis. I studied for ORA, ...
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1answer
26 views

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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27 views

reactomePA dataset

I tried to create my geneList according to this r code: setwd("C:/cygwin64/home/DIANGO/EXCELL/") d = read.csv("PA_down_id.csv",sep = " ", header = F) head(d) ...
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12 views

Pantherdb Export

After a gene enrichment analysis in the panther database I would like to export my graphic data (barplot and Pielot). Then I would be happy with a suggestion or advice from which will allow me to ...
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1answer
63 views

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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73 views

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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23 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
39 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
30 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
48 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: ...
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1answer
41 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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210 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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96 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 ...
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1answer
158 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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132 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
54 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 ...
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2answers
162 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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2answers
531 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 ...