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