Question: Transcriptome Microarray Database
0
gravatar for Anima Mundi
8.1 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

Hello,

could you suggest me a database of transcriptome microarray data? I would prefer data already presented in lists of altered transcripts (i. e. ESTs). Am I asking too much?

ADD COMMENTlink modified 8.0 years ago by Sean Davis25k • written 8.1 years ago by Anima Mundi2.4k
1

Honestly, I do not want to disturb here, but if you say "please put a little more effort" you assume bad faith. I checked the question accurately before publishing it; obviously, this does not mean I reached adequacy for sure. It is the first time I deal with microarray databases, possibly I made some mistake. In my opinion, your behavior leads to the exclusion of apprentices, and please note that I am just quite new to bioinformatics, not to molecular biology closely related to this topics. Other people could experience really greater problems and will not "dare" to ask something here.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
1

Your question is ambiguous because of the mix of wording. Transciptomes, microarrays, and ESTs are all separate, albeit related, concepts and techniques. A transcriptome is all RNA transcriptions of genes in a genome; microarrays measure the expression of a subset of the transcriptome; ESTs are sequences from reverse-transcriptions of transcripts, and can be used to construct probes for a microarray.

ADD REPLYlink written 8.1 years ago by Gotgenes460

Anima, please put a little more effort into phrasing proper questions. From your last 3 that I remember, I had a hard time understanding what you actually want to know every time.

ADD REPLYlink written 8.1 years ago by Michael Schubert6.9k

Apologies if it came off like that, questions on every level are of course perfectly fine. The issue is that in order to get good answers, it is beneficial if your question is easy to understand (e.g., by providing a bit more background information, tell us what already searched for and what you found, or what your current understanding of the topic is).

ADD REPLYlink written 8.1 years ago by Michael Schubert6.9k

I am conscious of the differences you are talking about, but thanks.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
5
gravatar for Neilfws
8.1 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

This type of question can be answered very easily using a simple web search.

There are only 2 such databases with which you need concern yourself: GEO and ArrayExpress.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Neilfws48k
2

I used the Search field before asking the question, I did not find what I wanted to know. In your faq you state this: "No question is too trivial or too "newbie". Please look around to see if your question has already been asked (and maybe even answered!) before you ask. But if you end up asking a question that has been asked before, that is OK and deliberately allowed". Thanks anyway.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
1

Sorry, I meant to type "web search" - amended. We should probably fix that FAQ :-)

ADD REPLYlink written 8.1 years ago by Neilfws48k

Yes, you really should: in particular, you should fix it before criticize.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
4
gravatar for Chris Evelo
8.1 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

Since you explicitly ask for analyzed and annotated data you might want to check out [?]The Gene Expression Atlas[?]. Which is:

"a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples."

So technically it is a subset of ArrayExpress but the semantic enrichment and the standardized statistics might make it useful for your purpose.

I was about to also advice the old Stanford Micorarray Database. But the site at http://smd.stanford.edu appears to dead. Does anyone know what happened to that? It was in fact the oldest public microarray database and did contain quite some data that did not appear in GEO or ArrayExpress especially on yeast. Update: I checked. The Google cached date is July 1, so it is probably just down.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Chris Evelo10.0k
1

There was a concerted attempt at NCBI GEO to import SMD data and I believe most SMD datasets have been imported.

ADD REPLYlink written 8.1 years ago by Sean Davis25k

Thanks a lot, Chris.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
3
gravatar for Sean Davis
8.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Another possibility is the MSigDB. If you are interested in human cancer, think about OncoMine.

ADD COMMENTlink written 8.1 years ago by Sean Davis25k

Thank you too, Sean.

ADD REPLYlink written 8.1 years ago by Anima Mundi2.4k
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