We have updated all the data sources that make up MitoMiner. Further details can be found here: http://mitominer.mrc-mbu.cam.ac.uk/release-4.0-beta/dataCategories.do
The biggest changes are:
IMPI - Integrated Mitochondrial Protein Index - Q3 2017
IMPI has had a major update - it uses more data and uses a different machine learning method (SVMs). The final list contains 1550 genes in human (1130 known and 420 predicted). To make MitoMiner easier to use each mammalian gene is now in one of the following categories (found in the summary header):
Known mitochondrial
Predicted mitochondrial
Predicted NOT mitochondrial
Known NOT mitochondrial
Probable contaminant
Dubious gene (pseudogenes, read-throughs etc.)
Mitochondrial diseases
We have also added a new mitochondrial disease section that provides additional information and links to the mitochondrial disorders pages at the Washington University Neuromuscular Disease Center http://neuromuscular.wustl.edu/mitosyn.html
New localisation datasets
We have also added four new localisation studies, three of which include sublocation information (Matrix, IMS etc.):
Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation.
Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY.
Elife. 2017 Apr 25;6.
PMID:28441135
Proteome analysis of human embryonic stem cells organelles
Shekari F, Nezari H, Larijani MR, Han CL, Baharvand H, Chen YJ, Salekdeh GH.
J Proteomics. 2017 Jun 6;162:108-118
PMID: 28435121
Landscape of submitochondrial protein distribution.
Vögtle FN, Burkhart JM, Gonczarowska-Jorge H, Kücükköse C, Taskin AA, Kopczynski D, Ahrends R, Mossmann D, Sickmann A, Zahedi RP, Meisinger C.
Nat Commun. 2017 Aug 18;8(1):290
PMID: 28819139
Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale.
Morgenstern M, Stiller SB, Lübbert P, Peikert CD, Dannenmaier S, Drepper F, Weill U, Höß P, Feuerstein R, Gebert M, Bohnert M, van der Laan M, Schuldiner M, Schütze C, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B.
Cell Rep. 2017 Jun 27;19(13):2836-2852
PMID: 28658629
Human Protein Atlas RNA tissue levels
RNA tissue levels from the Human Protein Atlas are now included in addition to the tissue antibody data
BioGRID
The interaction networks have been retired due to lack of use and maintenance difficulties. If you use this data please get in touch.
Thank you to everyone who made suggestions - your feedback makes MitoMiner better! If you have any questions or comments you can write to us at mitominer@mrc-mbu.cam.ac.uk.
