Tumor Rna Expression Databases
5
7
Entering edit mode
14.2 years ago
Ashwin ▴ 70

Looking for tumor RNA profile databases where I can study and compare expression levels of various levels of repair genes.

gene expression database cancer • 8.0k views
ADD COMMENT
11
Entering edit mode
14.2 years ago

To download microarray data, the first stop is GEO Datasets (http://www.ncbi.nlm.nih.gov/gds). You can search by tumor type, organism, platform, pubmed ID etc. Anyone publishing microarray data has to make it publically available, and that is the most popular place. There is also the ArrayExpress website for those who prefer the EBI (http://www.ebi.ac.uk/arrayexpress/), though I tend to find ArrayExpress to be a subset (albeit a slicker looking subset) of GEO. You can browse the normalized data directly on some of the GEO datasets without even downloading, though it's straightforward to pull the data directly from their FTP site or via various tools such as R.

ADD COMMENT
0
Entering edit mode

[?] The GEOmetadb and GEOquery BioConductor packages can be useful for searching and pulling into R, respectively. [?]

ADD REPLY
0
Entering edit mode

You can do specialized blast on GEO (link in BLAST homepage).

ADD REPLY
0
Entering edit mode

I was told that the reason Arrayexpress is a subset of GEO is that they make their content easily available to GEO to include while that is not done the other way around. That is something you should keep in mind when submitting data to any of them. I prefer not to punish a data provider for a more Open Data approach.

ADD REPLY
6
Entering edit mode
14.2 years ago

http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=189

You can also try to correlate these expressions to the Amplification data provided by the CONAN tool available at the Sanger website.

ADD COMMENT
6
Entering edit mode
14.2 years ago
D. Puthier ▴ 350

Have a look at: - geneSapiens - ArrayExpress - oncomine - TBrowser

ADD COMMENT
5
Entering edit mode
13.8 years ago

One of the most authoritative resources for this is CGAP and CGCI from the (US) National Cancer Institute. The NCI's Cancer Genome Anatomy Project sought to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient. Resources generated by the CGAP initiative are available to the broad cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find "in silico" answers to biological questions in a fraction of the time it once took in the laboratory.

There are several links to all types of data and tools: genes, chromosomes, tissues, SAGE Genie, RNAi, pathways and tools.

This should provide you with a lot of data with a specific cancer focus.

ADD COMMENT
0
Entering edit mode
10.6 years ago

Genevestigator contains a wide compendium of gene expression in cancer. It recently got mapped to the ICD-10 and ICD-O-3 classification. User friendly tools allow you to compare expression across various cancer types and compare with normal, non-tumor tissues.

https://www.genevestigator.com/gv/index.jsp

ADD COMMENT

Login before adding your answer.

Traffic: 1519 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6