Question: Online Resources For Mouse Research
16
gravatar for Andrew Su
5.2 years ago by
Andrew Su4.6k
San Diego, CA
Andrew Su4.6k wrote:

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

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.

ADD COMMENTlink modified 5 months ago by LLTommy790 • written 5.2 years ago by Andrew Su4.6k
2

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

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k

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

ADD REPLYlink written 5.2 years ago by Neilfws46k
10
gravatar for Mary
5.2 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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/

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Mary11k
1

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

ADD REPLYlink written 5.2 years ago by Mary11k

+1 for the excellent JAX.

ADD REPLYlink written 5.2 years ago by Neilfws46k

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?

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k

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.

ADD REPLYlink written 5.2 years ago by Mary11k
6
gravatar for Pierre Lindenbaum
5.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum91k wrote:

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

ADD COMMENTlink written 5.2 years ago by Pierre Lindenbaum91k
1

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.

ADD REPLYlink written 5.2 years ago by Larry_Parnell15k

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?

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k

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

ADD REPLYlink written 5.2 years ago by Pierre Lindenbaum91k

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!

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k

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.

ADD REPLYlink written 5.2 years ago by Larry_Parnell15k

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...

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
6
gravatar for Pascal
5.2 years ago by
Pascal1.4k
Barcelona
Pascal1.4k wrote:

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

ADD COMMENTlink written 5.2 years ago by Pascal1.4k

nice, added above!

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
4
gravatar for Alex Paciorkowski
5.2 years ago by
Rochester, NY USA
Alex Paciorkowski3.2k wrote:

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.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Alex Paciorkowski3.2k

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

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k

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

ADD REPLYlink written 5.2 years ago by Alex Paciorkowski3.2k
4
gravatar for Larry_Parnell
5.2 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

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

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Larry_Parnell15k

very good point. RGD added above!

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
4
gravatar for Dritoshi
5.2 years ago by
Dritoshi40
Kobe, Japan
Dritoshi40 wrote:

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.

ADD COMMENTlink written 5.2 years ago by Dritoshi40
3
gravatar for Casey Bergman
5.2 years ago by
Casey Bergman17k
Manchester, UK
Casey Bergman17k wrote:

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/

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Casey Bergman17k

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

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
1
gravatar for Qdjm
5.2 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

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

ADD COMMENTlink written 5.2 years ago by Qdjm1.9k

added to the list!

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
1
gravatar for Rainer
5.2 years ago by
Rainer10
Rainer10 wrote:

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.

ADD COMMENTlink written 5.2 years ago by Rainer10
1
gravatar for Leandro Batista
5.0 years ago by
Paris
Leandro Batista100 wrote:

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/

ADD COMMENTlink written 5.0 years ago by Leandro Batista100
0
gravatar for drsbello
4.8 years ago by
drsbello0
drsbello0 wrote:

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

ADD COMMENTlink written 4.8 years ago by drsbello0
0
gravatar for LLTommy
5 months ago by
LLTommy790
LLTommy790 wrote:

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.

ADD COMMENTlink modified 5 months ago • written 5 months ago by LLTommy790
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