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Listing a pre-known set of genesets

If you already have a list of GeneSet IDs off-site, but want to list them or add them all to a project, the simplest way to do so is with this URL:
http://geneweaver.org/index.php?action=search&gs_ids=<####,####,####,####...>

Getting all the genes from a set of genesets

Once you have a project (see above if you just have a list), you can get a matrix of genes by submitting a HiSim Graph. This will bring you to a page with a URL like either of the following:
http://geneweaver.org/index.php?action=analyze&cmd=watch&run=831b6155f8265590b697de67bc2d44ec
http://geneweaver.org/index.php?action=analyze&cmd=view&run=a4aacdc0a49836da5efe6195a6b5f239
The key here is the 32 characters at the end, copy them and type in the following by hand (obviously replace the a4...39 with your own):
http://geneweaver.org/results/a4aacdc0a49836da5efe6195a6b5f239.odemat
This .odemat is tab-separated, so should load into Excel. The first two columns are the internal GeneWeaver gene identifier (used in low-level code) and corresponding gene symbol displayed in output. The first two rows are the GeneSet ID number and GeneSet Label. In the top-left is the number of genes and number of GeneSets in the matrix.
Other possible files are:
  • .el - the edge list provided to biclique to generate a HiSim Graph
  • .el.profile - summary statistics about the .el graph from biclique
  • .bic - the list of node intersections displayed in the HiSim Graph
  • .dot - the GraphViz DOT input file used to generate the image (available in both HiSim Graph and GeneSet graph tools)

How to Manually reproduce GeneWeaver's "MeSH GeneSets"

This is a lot of work to do by hand, that's why we used the NCBI e-utilities to script most of it. But, if you want to create GeneSets using a similar technique, here is how it is possible:

  1. Search pubmed.gov for your mesh term using the field restriction:

ex: "Alcoholism"[Mesh]

  1. Click on "Display Settings", select "PMID List" and 200 Items per page, then click Apply. (see Large Result Caveat below)
  2. Copy all PMIDs into your clipboard (or a document).
  3. Go to Entrez Gene's advanced search page at http://www.ncbi.nlm.nih.gov/gene/advanced
  4. Change the first "All Fields" drop-down to say "PubMed ID", then paste the PMIDs you copied in step 3 into the adjacent box. Then click on the Search button.
  5. The resulting list of genes will be those annotated to publications annotated with your MeSH term of interest. You will most likely get some warnings due to PubMed IDs not linked to any genes, but these are safe to ignore. You can download this list of genes by using "Send to:" and selecting "File" and "UI List" - this will give you a list of Entrez Gene IDs which can be uploaded to GeneWeaver.

Large Result Caveat

If your search in step 1 finds more than 200 results, then step 2 will only show the first 200. If you want to do all by hand, then use the "Send to" option to download a File using the "PMID List" Format. In step 5 you will have to submit subsets of the resulting file since the full list will most likely be too large of a query.

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