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I was wondering whether anyone could suggest sources of information about amplified genes in cancer, especially if the website tries to combine it with (over)expression information. We wrote a review on amplified and expressed genes recently and are trying to get a sense of what else is out there, so that when we update it we make sure we get different sources of information, not just a search of the literature.
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It would be helpful if you listed the sources that you already have (for the benefit of other users who find this thread and to prevent duplication of resources you are already aware of).
That being said some resources that spring to mind are listed below. Mostly these are initiatives that have created or are in the process of creating data that would provide both amplification and expression data, via next generation whole genome shotgun (WGS) and RNA sequencing (RNA-seq) or copy-number + expression microarrays.
Oncomine [registration required]
The Cancer Genome Anatomy Project (CGAP)
The Cancer Genome Characterization Initiative (CGCI; may soon have relevant data)
The Cancer Genome Atlas (TCGA; relevant data gradually entering the public domain)
The international cancer genome consortium (ICGC)
The database of genomic variants -
Here is a list of the ones we have got already- CONAN (http://www.sanger.ac.uk/cgi-bin/gene...nan/search.cgi)
- Cancer Genome Workbench (https://cgwb.nci.nih.gov/)
- Breast (http://www.itb.cnr.it/breastcancer/)
- Integrative Oncogenomics Cancer Browser - IntOGen (http://www.intogen.org/)
- Oncomine (http://www.oncomine.org/)
Oh, and of course there is our website too: http://amplicon.icr.ac.ukLast edited by danielsbrewer; 09-23-2010, 12:40 AM.Comment
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We've put together a resource which allows one to query for over-expression and amplification in Cancer genomics samples, particularly those profiled by The Cancer Genome Atlas.
Here are some related threads if you're interested:
Good luck!
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Products @ www.stationxinc.comLast edited by GenePool; 11-23-2014, 09:26 PM.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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