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It's my first time posting to this forum but was looking for some help on the data aspects of this project.

My tools of choice would be in python/R .

Goal: I'm looking to create a disease specific profile of just SNPs and SNPs in miRNAs and miRNA target sites.

PART 1: TCGA My first step is using TCGA data which lists a ton of harmful mutations in a LOH .txt format. I'd like to be able to map those mutations to SNPs or genes or miRNAs (whatever entities they belong to). The TCGA datasheet is here. Example data is here. for breast cancer. I guess I can use this miRNA and mRNA data as well.

Questions here:

  1. How to decipher the LOH data to figure out if it's meaningful and where it maps?
  2. Which Tools to use for mapping and what formats for final data ? Fasta ?

miRNA/Targets and SNPs Next up is getting cancer specific miRNAs and mRNAs and mapping SNPs to them? I'm assuming using dbSNP or Sanger miRNA databases to get miRNA/targets and seed sequences.

I'm a bit lost as how to combine all these pieces of information, what formats to use for output (linked to individual pieces) and which tools if any to use to gather all this data using python. This tool is useful tool mirdsnp.

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  • $\begingroup$ I think you might be missing a few links - I don't see your TCGA datasheet and I can't tell whether the last sentence is meant to have a link or not. $\endgroup$
    – blep
    May 18, 2013 at 22:30
  • $\begingroup$ Hi I edited it. I believe I was only allowed one link so hopefully it's fixed.. here is the [data sheet][1] I guess my issue is understanding how to make sense of the LOH data and how to map it in a meaningful way.. The second is how to incorporate the miR and miRsnp related data. Thanks for catching the missing links. If I wasn't clear enough or didn't provide enough information let me know and i'll clarify as much as I can [1]: tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp $\endgroup$
    – prussiap
    May 19, 2013 at 0:37
  • $\begingroup$ I can't comment on the science, but as far as the analysis goes, Biopython has great tools for working with FASTA-formatted data: see SeqRecord $\endgroup$
    – blep
    May 19, 2013 at 1:19

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You can take a look at this tutorial to understand TCGA MAF files. And you can find a list of TCGA MAF files containing mutations mapped to genes and miRNA at https://www.synapse.org/#!Search:syn1710680

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  • $\begingroup$ Thanks for the answers. @dd3 I was planning on using SeqRecord. Though I'm not sure how to add features to SNPs to link them to associated miRNAs or targets etc.. $\endgroup$
    – prussiap
    May 19, 2013 at 4:00
  • $\begingroup$ those are great links. How did you deduce the MAF. I'm looking at SNP and expression miRNA profiling for level 3 [tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp data]. for where I found that information and it mentions LOH and MAGE-TAB. Here is another [broadinstitute.org/collaboration/gcc/data/data-types link] .. So i guess for this particular part I'm confused about data format, and meaning of the data :) . For the rest it's how to manipulate miRNAs and then batch search with python/biopython. Thanks again. $\endgroup$
    – prussiap
    May 19, 2013 at 4:05
  • $\begingroup$ Affter finding this [wiki.nci.nih.gov/display/TCGA/Accessing+MAF+files link] it seems to me that level 2 files are MAF files. Level three are .txt something else. $\endgroup$
    – prussiap
    May 19, 2013 at 4:09
  • $\begingroup$ @prussiap: I'm not familiar with the file formats, but could you use Python dictionaries, using SNP IDs as keys? $\endgroup$
    – blep
    May 19, 2013 at 7:23
  • $\begingroup$ That is the method I am using so far. This does remove duplicates but I still would like to do a mass download of positions and annotations for each SNP. $\endgroup$
    – prussiap
    May 20, 2013 at 22:10

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