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Old 04-19-2016, 03:36 AM   #1
BeKl
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Default Differential Expression "categorisation"

Hello!
Some weeks ago my group did an RNA-sequencing project to get information about differentially expressed genes in 2 cell types of an algae. After the mapping of the reads to the reference genome, expression analysis was performed using ReadXplorer and DESeq. Now I have an Excel file containing a list of gene names and corresponding BaseMean values / fold change values.

As a next step i would like to have an analysis, which groups of genes are up-/downregulated in cell type A / B (compared to the other one). I imagine a figure with groups of genes (like "mitosis related" or "Photosynthesis related") on the X-axis and "number of genes up-/downregulated in cell type A / B" on the Y-axis. Can someone suggest an easy to use freeware to do this analysis (not the picture, just the "categorisation") ? I am new to bioinformatic analysis like this and would be thankful to get some advice!

Best regards,
BeKl
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Old 04-19-2016, 03:47 AM   #2
dpryan
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You're looking for "gene ontology" or "pathway" analysis. I think "David" is the most popular online tool, though there are a LOT of them if you google any of the aforementioned terms.
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Old 04-19-2016, 03:58 AM   #3
GenoMax
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@Devon: There is some question about viability of DAVID (last updates appear to have been in 2010).

It is unclear to me if anyone is actually managing DAVID or if the website is running on autopilot. Email sent to DAVID related email address asking about the status of updates to annotation has so far failed to elicit any response.
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Old 04-19-2016, 06:12 AM   #4
dpryan
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Eeek, I hadn't realized that. Given its popularity that's seriously disappointing.
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Old 04-19-2016, 06:33 AM   #5
GenoMax
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It would be best if someone (on SeqAnswers) knows folks @NIH who can track down the DAVID people (if there are any left .. on Biostars it was suggested that a contracting company was working on DAVID for a while and may no longer be doing that).
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Old 04-19-2016, 06:40 AM   #6
dpryan
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Maybe Sean Davis knows? He's at least at NIH.
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Old 04-19-2016, 09:05 AM   #7
BeKl
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Thanks for the quick answers. Yes, DAVID seems to be what I am looking for, but there is one problem: the gene IDs in my list are phytozome IDs... as far as I can see, the DAVID tools do not support phytozome IDs (for example the "Gene ID Conversion Tool ").
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Old 04-19-2016, 08:59 PM   #8
wdecoster
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Very up to date and nicer features than DAVID: http://amp.pharm.mssm.edu/Enrichr/
(I have no relationship to that website but I am a huge fan and use it daily)
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Old 04-20-2016, 06:39 AM   #9
fanli
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As much as I love DAVID, I do agree it's a bit dated. @wdecoster that looks cool - I'll have to check it out too!

My limited experience with Ingenuity has been promising as it does have a lot of functionality and annotation that isn't widely available. But you'll have to see if you have institutional access...
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Old 04-20-2016, 09:05 AM   #10
BeKl
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Again, thank you all for your advice - these tools seem to be the right ones, but there is still my problem with the IDs...
The genome and the gene sequences / annotations are only available in phytozome (a database for algal genomes) and there are no corresponding genbank IDs (which I need for the analysis-tools, right?)
Does anyone have a solution for this?
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Old 04-20-2016, 09:24 AM   #11
fanli
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Can you do the enrichment analysis in Phytozome itself? I think that might be easiest...
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Old 04-20-2016, 11:27 AM   #12
marRoma
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Hi,

i found your post , i have a similar problem with genes IDs in David... they are based on KEGG database but David does not recocognize it and the genes locus changed in genbank recently... did you fix your problem? do you have any suggestions?

thank u
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