User: Ambika
Ambika • 40
- Reputation:
- 40
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- New User
- Location:
- United States
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 3 years, 4 months ago
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Posts by Ambika
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... Hello everyone,
I am trying to do gene enrichment analysis on some predefined set of genes. For this I tried to annotate those genes against the swissprot and nr database. I tried to import the xml blast output (out format 5) in omics box. I was able to perform the mapping and GO annotation easily ...
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... Can it interpret the KEGG ids and assign the pathways associated with it? ...
written 3 months ago by
Ambika • 40
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... Hello everyone,
I do have file with gene list and corresponding KO Id from KEGG pathway analysis which looks like this:
FUN_000082-T1
FUN_000109-T1 K00799
FUN_000143-T1
FUN_000188-T1
FUN_000231-T1
FUN_000233-T1
FUN_000387-T1
FUN_000399-T1 K00637
FUN_000399-T ...
written 3 months ago by
Ambika • 40
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... Yes I want the p-values and the gene id (FUN__) in my results, which I am not getting. Thank you for the link, I will check that one. ...
written 3 months ago by
Ambika • 40
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... Kevin, I think I do have a list as mentioned in the protocol. The list looks like this
> head(gene2GO)
$`FUN_000109`
[1] "GO:0005515" "GO:0005515" "GO:0005515" "GO:0005515"
$FUN_000399
[1] "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374" "GO:0008374"
...
written 3 months ago by
Ambika • 40
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... Kevin,
This is how my input files looks like:
GO_total_upregulated_genes.csv
GeneID Goterm
FUN_004018 GO:0016491
FUN_004018 GO:0046872
FUN_004018 GO:0055114
FUN_003797 GO:0000287
FUN_003797 GO:0030976
FUN_003797 GO:0030976
FUN_00379 ...
written 3 months ago by
Ambika • 40
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... Hello everyone,
I am working with a non-model fungus and trying to do gene enrichment analysis for differentially expressed genes. For this I got the GO terms for a list of genes using InterProscan. Now I am using these list of genes with respective GO terms to do enrichment analysis and to make pl ...
written 3 months ago by
Ambika • 40
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255
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... The program I am going to use does the hierarchical distribution based on p-value so I don't think I can do that. I need an exact p-value. ...
written 4 months ago by
Ambika • 40
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... I am doing gene enrichment analysis of differentially expressed genes using TopGO for which I need p-value of the listed genes. In my case I have 3 different p-values from three timepoints. I am looking for a way to combine these p-values to one so that I can proceed further. ...
written 4 months ago by
Ambika • 40
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... Hello everyone,
I have the list of differently expressed genes from DESeq2 for three different timepoints. I have few genes that are differentially expressed in all three timepoints for which I want to combine the p-values to get one. I was thinking of taking an average p-value, but looks like that ...
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