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Questions tagged [go-enrichment]

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Multi Factor in Deseq2 Gene enrichment analysis

I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table. ...
ToTheMoon's user avatar
2 votes
1 answer
59 views

How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?

I am working on using WGCNA for a bulk RNA-seq experiment. I have three experimental conditions (control, treatment 1, and treatment 2) and have a total sample size of 18 (6 per group). Using the ...
Meena Easwaran's user avatar
0 votes
1 answer
45 views

GO Enrichment Analysis

I want to annotate 25,000+ proteins with GO_ID, TERM, and CATEGORY prior to doing enrichment analysis. Can I extract this information by submitting my sequences? Meanwhile, my species is a fish, and ...
Kishor Kumar Sarker's user avatar
1 vote
1 answer
75 views

Enrichment analysis of DMPs | new Ilumina EPIC V2 900K

Im analyzing methylation data from the new illumina's EPIC V2 array (900K). I would like to perform enrichment analysis on DMPs. In the past, I have always used missMethyl but since there are a lot of ...
Julieta's user avatar
  • 21
1 vote
0 answers
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enrichment of DE genes within wide regions not pathways, hypergeometric test or GSEA?

I haven't found any relevant posts, so here is my question (it's more a question on statistics I believe): I have the deseq2 output of DE genes( around 25000 genes) , and among them 1000 are ...
dew's user avatar
  • 11
1 vote
1 answer
54 views

Gene Set Comparison Without Expression Data

I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
Eliza R's user avatar
  • 11
0 votes
0 answers
16 views

overrepresentation test, between transcriptome and candidates sequences obtained from the transcriptome

For an analysis of my data, I have a transcriptome and a list of sequences obtained from the transcriptome. I would like to perform a functional enrichment analysis. I have annotated both sets of data ...
se-tima's user avatar
  • 21
1 vote
1 answer
27 views

How to get enriched pathways in the data using continous statistic measure?

I was doing pathway enrichment analysis using the below code ...
Megha's user avatar
  • 395
2 votes
0 answers
109 views

COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results

I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the ...
se-tima's user avatar
  • 21
1 vote
0 answers
33 views

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. ...
mmpp's user avatar
  • 371
0 votes
1 answer
53 views

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 ...
user324810's user avatar
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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....
Spartan 117's user avatar
1 vote
1 answer
137 views

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 ...
Gee3's user avatar
  • 11
0 votes
1 answer
43 views

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 ...
Spartan 117's user avatar
0 votes
0 answers
40 views

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 ...
gabt's user avatar
  • 348
0 votes
1 answer
462 views

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 ...
user9656's user avatar
2 votes
1 answer
147 views

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 ...
Mee's user avatar
  • 81
1 vote
1 answer
92 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 ...
Anna Maria Bugaj's user avatar
5 votes
1 answer
372 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 ...
Darío Rocha's user avatar
2 votes
0 answers
305 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 ...
0x90's user avatar
  • 1,437
1 vote
0 answers
51 views

How to detail the specific GO terms

How can I get more specific GO terms when using clusterProfiler? I got my Dotplot by: ...
hua's user avatar
  • 441
0 votes
2 answers
46 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 ...
hua's user avatar
  • 441
0 votes
1 answer
48 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 ...
Tapper's user avatar
  • 67
0 votes
3 answers
60 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: ...
Lin's user avatar
  • 29
1 vote
1 answer
255 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 ...
plat's user avatar
  • 1,042
1 vote
2 answers
1k views

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, ...
Nova's user avatar
  • 165
1 vote
0 answers
324 views

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 ...
yepp's user avatar
  • 11
4 votes
1 answer
214 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 ...
benn's user avatar
  • 3,571
3 votes
2 answers
79 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 ...
Reilstein's user avatar
  • 367
6 votes
2 answers
296 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 ...
julianstanley's user avatar
5 votes
2 answers
915 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 ...
aluriak's user avatar
  • 161