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8.5 years ago
Learner
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280
Hello,
I would like to know if there is any tool to download the sequences of all proteins which were unregulated in cancer. if even we cannot retrieve those that up regulated and down regulated. how one can download all proteins for e.g. metastatic cancer of specific organism
Download all proteins. Seriously, since you can only get funding if you somehow relate your work to cancer, available data is so biased that almost all proteins people have worked on have some link to cancer. Otherwise, you'll have to be more precise in your question.
@Jean-Karim Heriche your comment is a bit offensive but I ignore since I am not here to discuss such stuff. My question was very clear. If I want to download bunch of proteins sequences I can do it through pubmed but I want to extract as much as possible through pubmed instead clicking on each of them separately. for example , you can set the pubmed to protein and then search this keyword (cancer) AND "Homo sapiens"[porgn:__txid9606] you can get 8902. then you can always make the list lower and lower and lower.
Sorry if you found the comment offensive. It was meant to make you think about the bias. If you're taking all kinds of cancers across all experiments ever done, you're most likely to come up with a significant portion of the genome. Anyway, you can have a look at Expression Atlas, filtering the descriptions for terms such as tumor. Another approach could be to look at genes in KEGG e.g. http://www.kegg.jp/kegg-bin/search?q=cancer&display=disease&from=disease
@Jean-Karim Heriche no problem dear! of course if I get proteins from different organism make no sense for analysis and that is Exactly why I ask the question here. what worries me is to end up with a list of 60000 sequences! . I am more searching for a tool that allows me to shrink down my search. for example, those that are specific for lung cancer , homo sapines and metastatic , I'll look at those links you have shared and I appreciate your comment by liking it, thanks
Have you thought in giving BioMart a go? You can search for a given phenotype (e.g. lung vasculature development) and get the genes and proteins associated with it. The issue here is with the phenotype ontology. We may have 'lung vasculature development' but also other types of phenotype including 'lung cancer'. This ontology lookup may be useful to investigate. Perhaps the EBI search could help you out as well? It's available via the web or programmatically with the RESTful.