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

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) – Synteny Blocks 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? 1.Do a Region Search, pasting in the three QTL regions. 2.Save the list of genes. 3.Find the genes annotated to “cytoskeleton”. 4.Save the list of genes. 5.Intersect the two lists. 6.Forward the result to Galaxy.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

26. 1. Click 2. Click

27. 1. Click 2. Select 3. Click