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MouseMine: Mouse Gene Lists (and a whole lot more)
Joel Richardson
www.mousemine.org
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
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
WormBaseZfin
MouseMine in Context
http://intermod.intermine.org
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
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.
Aside: MouseMine supports work flows
plug-insave
download
upload
forward
xlstsvxmljson
filter/sort/add/remove cols.
Template / Query
List
union/intersection/diff
IDs
download
forward
xlstsvxmljson
run
1. Click
1. Do a Region Search, pasting in the three QTL regions.
1. Click
2. Click
3. Type or paste
4. Click
1:147249520-1830922346:115242853-14642923818:52833084-68645706
1. Do a Region Search, pasting in the three QTL regions.
For this example, we only want the genes.
1. Click
2. Save the list of genes.
1. Click
3. Find the genes annotated to “cytoskeleton”.
1. Click
2. Click
3. Find the genes annotated to “cytoskeleton”.
1. Type
2. Click
3. Find the genes annotated to “cytoskeleton”.
1. Click
4. Save the list of genes.
4. Save the list of genes.
1. Type
2. Click
4. Save the list of genes.
1. Click
5. Intersect the two lists.
1. Click
2. Click
3. Click
4. Click
5. Type6. Click
5. Intersect the two lists.
1. Click
6. Forward the list to Galaxy
1. Click
6. Forward the list to Galaxy
1. Click
2. Click
6. Forward the list to Galaxy
1. Click
6. Forward the list to Galaxy
BONUS: What are all the phenotypes associated with those 58 genes?
1. Click
2. Click
1. Click
2. Select
3. Click
