8 votes
Accepted

Clarification on Gene Enrichment

If you compare A vs B the genes's fold change will have the opposite sign to B vs A. So will be the gene set up or down-regulated depending on the comparison to take. The gene set test analyze if a ...
llrs's user avatar
  • 4,693
5 votes

Clarification on Gene Enrichment

While I'm not familiar with GSEA software in particular, I believe your problem is that it only tests for upregulated gene sets. Notice: 866/4408 gene sets are upregulated 3542/4408 gene ...
juod's user avatar
  • 473
4 votes

GOseq analysis with evidence code filter

A bit weird to answer my own question, but for who's interested I can show the 'hard' way using biomaRt and then use goseq with <...
benn's user avatar
  • 3,571
3 votes
Accepted

How to run enrichment analysis of protein functional annotation?

DAVID depend on a couple of databases from the Gene Ontology Consortium, Reactome, KEGG,... most of them are accessible via Bioconductor. To perform an enrichment analysis you can have a look at the ...
llrs's user avatar
  • 4,693
3 votes

How to run enrichment analysis of protein functional annotation?

I would recommend R instead of sticking to websites. There are many tools for enrichment analysis. I like to use GOseq, which is initially made for RNAseq data, but can also be used for proteins (I ...
benn's user avatar
  • 3,571
2 votes

Alternative to enrichR for enrichment analysis?

Try gProfileR. It is very intuitive and easy to use in R.
plat's user avatar
  • 1,032
2 votes

Alternative to enrichR for enrichment analysis?

A couple of years ago I wrote a blog post about GSEA methods in Bioconductor, in addition to these I would recommend clusterProfiler or ReactomePA. In most of them you need to provide the gene set/...
llrs's user avatar
  • 4,693
2 votes

Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

I tinkered with a program GSEA-SNP quite a few years back, which claims that it does a similar ranking procedure with SNPs. It carries out its procedure by first linking SNPs with genes, then running ...
gringer's user avatar
  • 13.9k
2 votes
Accepted

are GSEA and other geneset enrichment analysis supposed to yield extremely different results between them?

Each of these methods do something different, so it is reasonable to expect different results. The bottom line is that there isn't a single question you can ask when you do an "enrichment test&...
llrs's user avatar
  • 4,693
2 votes

How to convert a list of genes to one element per row?

$ echo "Mtss1/Sox11/Fbn2/Mmp2/..." | tr '/' '\n' > list.txt For more information on tr: https://en.wikipedia.org/wiki/Tr_(...
Alex Reynolds's user avatar
2 votes
Accepted

What type of Protein ID is this?

I'm not sure I understand the question, but XP_019970915.1 is an 'NCBI Reference Sequence' ID for 'erythrocyte binding antigen-181' (https://www.ncbi.nlm.nih.gov/protein/XP_019970915.1/). If you look ...
jared_mamrot's user avatar
2 votes
Accepted

less than 80% of your list has mapped to your chosen identifier type

DAVID last received an update in May 2016 (https://david.ncifcrf.gov/content.jsp?file=update.html), so any additions to the Gene Ontology database since then won't be present. I checked the examples ...
Devon Ryan's user avatar
  • 19.6k
2 votes

Multi Factor in Deseq2 Gene enrichment analysis

If you don't tell DESeq what contrast to make, it just does the default contrast. Which is your reference versus the last other one alphabetically.
swbarnes2's user avatar
  • 1,900
1 vote

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

Consider filtering on every parameter: Gene Significance (GS), p-value for Gene Significance (p.GS), Module Membership (MM), and p-value for Module Membership (p.MM). This doesn't mean you need to ...
BigMistake's user avatar
1 vote

Gene Set Comparison Without Expression Data

You can't do a GSEA on a set alone because the differentiating statistic (or, occasionally, the rank) is used to calculate the enrichment score that is produced by the GSEA algorithm. The other gene ...
gringer's user avatar
  • 13.9k
1 vote
Accepted

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

Just to mention I personally think there is a higher loop above the loop stated above. I've not looked at each bit of code in detail but there's a bug is on line 4: ...
M__'s user avatar
  • 12.1k
1 vote
Accepted

Does it make sense to perform pathway enrichment analysis on a list of mutated genes from a VCF?

The concept of looking for enriched pathways makes sense, but you can't do it using the same tools you would use for gene expression data because the biases are different - longer genes are far more ...
Ian Sudbery's user avatar
  • 3,321
1 vote

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

The answer to your main doubt about "annotation vs. enrichment" is that you need both, but you already have one annotation. You can only perform a functional enrichment analysis after you ...
Lucio Queiroz's user avatar
1 vote

Compare functional enrichment between genelists

To compare gene list based on gene ontologies you can use GOSemSim (Note, I'm a contributor to the package). You can select the semantic similarity to compare them, that is how the redundancies and ...
llrs's user avatar
  • 4,693
1 vote
Accepted

about GO terms's name

The various Gene Ontologies are arranged as Direct Acyclical Graphs. This means that each term can have children and parents. When a gene is annotated with a GO term, it also inherits all of that term'...
terdon's user avatar
  • 9,846
1 vote
Accepted

Why are my genes filtered for Gene Ontology term enrichment?

What is "click here for details" saying? That link should contain an explanation of what happened. GSEA usually requires entrez_id to run. If your list contains <...
fra's user avatar
  • 567
1 vote

How to convert a list of genes to one element per row?

In R you can use tidyr's function separate_rows. ...
benn's user avatar
  • 3,571

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