Online Resources For Mouse Research

Question

[Andrew Su]

I'd like to create a collection of the most useful online resources for mouse researchers. Here's my list so far...

• Pathway and network resources
  • STRING
  • IntAct
  • WikiPathways
  • Pathway Commons
  • Reactome
  • KEGG
  • GeneMANIA
• Genomics resources
  • KOMP - knockout mice
  • IMSR - mouse strains and stocks
  • Cre-X-Mice - Cre transgenic mouse lines
  • MMRRC - mutant mice and ES cell lines
  • UCSC Genome browser
  • Ensembl
  • NCBI Gene
  • MGI
  • TIGM - mouse knockout database
  • IGTC - gene trap cell lines
  • GeneNetwork - genotypic variation and covariation
  • PhosphoSite - post-translational modifications
  • Mouse Genomes Project - whole genome sequence for common strains
  • Rat Genome Database - includes data for mouse phenotypes, QTL, etc.
  • Mouse Strain SNPs
• Phenotype resources
  • LAMHDI - animal models
  • caMOD - animal models of cancer
  • EMPReSS - mouse phenotyping SOPs
  • Europhenome - mouse phenotypes
• Expression resources
  • GXA
  • Allen Brain Atlas
  • e-Mouse Atlas
  • Circadian Expression Profiles
  • GENSAT
  • Genepaint
  • Eurexpress - mouse embryo
  • NIH Neuroscience Consortium - not actively updated?
  • Interactive 3D Mouse Limb Anatomy Atlas
• Other
  • The Visible Mouse Project - anatomy reference
• Meta-resources
  • Mouse Resource Browser
  • BioGPS

I'm bolding the links that have at least some specificity for mouse (and personally, I'm particularly interested in more like these). I've also tried to roughly group the resources by category, but these are very approximate.

Note that this is similar to my previous question, but this specifically focuses on resources for mouse researchers and isn't limited to gene-centric ones.

[Andrew Su]

would you like some toh-may-toh with your toh-mah-toh? okay, okay, I edited to be more precise...

[Neilfws]

I'd say this list focuses on tools useful to mouse researchers, not specifically on mouse resources.

Answer 1

[Mary]

Mouse resource browser: http://bioit.fleming.gr/mrb/

Jax: http://informatics.jax.org/

Edit: Gensat: http://www.ncbi.nlm.nih.gov/projects/gensat/

eMICE: http://emice.nci.nih.gov/

caMOD: http://cancermodels.nci.nih.gov/camod/

LAMHDI: http://lamhdi.org/

[Mary]

close to my heart, I was a postdoc there--on the gene expression database :)

[Neilfws]

+1 for the excellent JAX.

[Andrew Su]

Thanks Mary... I added all of these to the list above except for eMICE, which seems like it's focused on education and outreach to the lay community, rather than researchers. Is that fair, or did I miss something?

[Mary]

Well, eMICE has links to other resources such as the phenotyping projects (in the characterization section) and to caBIG and such. But that's been covered elsewhere now too. Another topic area that might be related--or too far from your goal--is colony management.

Answer 2

[Pierre Lindenbaum]

Fantom : http://fantom.gsc.riken.jp/3/

[Larry_Parnell]

FANTOM is an important resource for lists of transcription factors. To me, this is the most complete list of TFs, but I only know this for human. Nonetheless, many human TFs have the same gene symbol, same function in mouse.

[Andrew Su]

Pierre, is it fair to say that the FANTOM site is more interesting for the historical context than current utility? or am I missing something?

[Pierre Lindenbaum]

no idea :-) That was the only resource I knew :-))

[Andrew Su]

Larry, forgive my ignorance, but have those lists of TFs not been translated into formal annotations elsewhere (e.g., GO)? Or is the FANTOM list still the go-to place for you? If the latter, can you post a direct link? Thanks!

[Larry_Parnell]

My source for FANTOM is Table S1, list of human TFs used by Ravasi (2010 Cell 140: 744-752) to describe transcription networks and interacting pairs.

[Andrew Su]

Ahh, good lead... Which ultimately led me to the FANTOM 4 project (http://fantom.gsc.riken.jp/4/), which inexplicably is not linked from the older FANTOM 3 page that Pierre posted above. Although many of the tools on the FANTOM 4 page appear to be non functioning (grumble grumble), there do appear to be tools that are theoretically useful...

Answer 3

[Pascal]

Great list! I suggest to add Sanger's Mouse Genomes project where you could find BAM files of 17 mouse strains.

[Andrew Su]

nice, added above!

Answer 4

[Alex Paciorkowski]

NIH Neuroscience Microarray Repository -- you can go to "navigate repository" and have access to the raw gene expression array data for ~100 mouse models of numerous (mostly neurologic) disorders.

[Andrew Su]

not clear to me if it's still updated (page says the project ended in 2010), but added it above anyway... Thanks!

[Alex Paciorkowski]

Nope, not updated, but the data are still present & obtainable. For now...

Answer 5

[Larry_Parnell]

I would add the Rat Genome Database because there are links - based on syntenic arrangements of genes, also diseases, phenotypes, and the like - between the mouse and rat genomes.

I also find the maps of genomes from mouse, human, and other organism genomes as displayed at NCBI useful, especially when comparing QTL and gene regions between human and mouse, with links to OMIM and cytogenetic map positions displayed.

Added in edit: GeneOntology.org for GO terms and search capability. This is where I've gone for genes with a specific GO annotation.

Added in 2nd edit: VISTA, a database of human enhancers functional in mouse embryogenesis. Also, PEDB: Mammalian Promoter/Enhancer DataBase.

Strains: International Mouse Strain Resource (IMSR) at http://www.findmice.org/ and at NCBI one can compare SNPs between mouse strains, which would be an aid in mapping phenotypes to genes from crosses.

Anatomy: EMAP Home - The Edinburgh Mouse Atlas Project at http://www.emouseatlas.org/emap/home.html [?] The Visible Mouse at http://tvmouse.compmed.ucdavis.edu/ [?] Interactive 3D Mouse Limb Anatomy Atlas, http://www.nimr.mrc.ac.uk/3dlimb

[Andrew Su]

very good point. RGD added above!

Answer 6

[Dritoshi]

BrainStars: http://brainstars.org/

BrainStars (B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.

Answer 7

[Casey Bergman]

The International Mouse Phenotyping Consortium should be added, and it would be good to add any other relevant resources from their links page like http://www.europhenome.org/ & http://empress.har.mrc.ac.uk/

[Andrew Su]

mouse phenotyping is a whole class of resources I didn't have before -- will integrate with the list above!

Answer 8

[Qdjm]

How about GeneMANIA: http://www.genemania.org ?

[Andrew Su]

added to the list!

Answer 9

[Rainer]

As you have KOMP, IGTC, MGI and the like on the list, I would strongly suggest adding the International Knockout Mouse Consortium (IKMC).

It's combining all major knockout mouse resources in one location, also EUCOMM and NORCOMM for example, which are not on your list.

Answer 10

[Leandro Batista]

Although not mouse specific, I'd say that PosMed is a great resource for positional cloning and other candidate gene approaches:

http://omicspace.riken.jp/PosMed/

Answer 11

[drsbello]

I'd also add: Mouse Phenome Database (MPD, http://phenome.jax.org/)

Answer 12

[LLTommy]

I am kind of surprised (shocked) that IMPC (International Mouse Phenotyping Consortium) is missing in that list http://www.mousephenotype.org/.

EDIT: Ok, another user mentioned it before, Andrew just did not update the list I guess.