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MouseMine : Mouse Gene Lists (and a whole lot more)

MouseMine : Mouse Gene Lists (and a whole lot more). Joel Richardson. www.mousemine.org. What can MouseMine do for you?. A ccess to latest mouse data from Mouse Genome Informatics (MGI) genes, functions, phenotypes, disease models,… P owerful querying and reporting tools

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MouseMine : Mouse Gene Lists (and a whole lot more)

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  1. MouseMine: Mouse Gene Lists (and a whole lot more) Joel Richardson

  2. www.mousemine.org

  3. What can MouseMine do for you? • Access to latest mouse data from Mouse Genome Informatics (MGI) • genes, functions, phenotypes, disease models,… • Powerful querying and reporting tools • many predefined queries • point-n-click query builder (not SQL!) • result displays: page/sort/filter rows, reorder/add/remove columns, download • Customization • customize/save your own queries • save/reuse lists of genes (or publications, or strains, or OMIM terms, or …) • mark your favorites • Bulk operations: • upload list of IDs • use lists of object to “drive” queries • download/forward the results • Integration with your workflow • Interactive or scripted use

  4. MouseMine in Context bio mart Acquisition ad hoc Integration reports Dissemination web MGI Mouse Mine SGD Yeast Mine Fly Mine InterMOD (HG004834) Rat Mine RGD Zebra Fish Mine WormMine Zfin WormBase

  5. http://intermod.intermine.org

  6. MouseMine contents • Mainly, the “annotation core” of MGI: • mouse genome catalog, alleles, genotypes, strains, cell lines, publications, cross references • Mouse function, phenotype, and disease annotations* • Smattering of human data: genes, coordinates, OMIM annotations • Plus: • Panther • MEDIC (*annotations mapped) • SyntenyBlocks • Coming soon: • expression data from GXD • gene models

  7. Why MouseMine? A Quick Example I have three QTL regions associated with radiation induced pulmonary fibrosis in mouse models. Are there any cytoskeletal genes in these regions? Do a Region Search, pasting in the three QTL regions. Save the list of genes. Find the genes annotated to “cytoskeleton”. Save the list of genes. Intersect the two lists. Forward the result to Galaxy.

  8. Aside: MouseMine supports work flows xls tsv xml json Template / Query download run forward filter/sort/add/remove cols. save plug-in union/intersection/diff forward List upload IDs xls tsv xml json download

  9. Do a Region Search, pasting in the three QTL regions. 1. Click

  10. Do a Region Search, pasting in the three QTL regions. 1. Click For this example, we only want the genes. 2. Click 3. Type or paste 1:147249520-183092234 6:115242853-146429238 18:52833084-68645706 4. Click

  11. 2. Save the list of genes. 1. Click

  12. 3. Find the genes annotated to “cytoskeleton”. 1. Click

  13. 3. Find the genes annotated to “cytoskeleton”. 1. Click 2. Click

  14. 3. Find the genes annotated to “cytoskeleton”. 1. Type 2. Click

  15. 4. Save the list of genes. 1. Click

  16. 4. Save the list of genes.

  17. 4. Save the list of genes. 1. Type 2. Click

  18. 5. Intersect the two lists. 1. Click

  19. 5. Intersect the two lists. 1. Click 4. Click 2. Click 3. Click 5. Type 6. Click

  20. 6. Forward the list to Galaxy 1. Click

  21. 6. Forward the list to Galaxy 1. Click

  22. 6. Forward the list to Galaxy 2. Click 1. Click

  23. 6. Forward the list to Galaxy 1. Click

  24. BONUS: What are all the phenotypes associated with those 58 genes?

  25. 1. Click 2. Click

  26. 1. Click 2. Select 3. Click

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