DOWNTIME: Thursday 9th November 2017

MitoMiner will be offline on Thursday 9th of September from 07:00 GMT for a few hours to allow the building's network connection to be upgraded. Sorry for the inconvenience.

DOWNTIME: Sunday 24th of September 2017

MitoMiner will be offline on Sunday 24th of September from 11:00 GMT for a few hours, to fix a couple of minor bugs. Sorry for any inconvenience. 

MitoMiner Updated! - September 2017

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 VLam SSUdeshi NDSvinkina TGuzman GMootha VKCarr SATing AY.

Elife. 2017 Apr 25;6.

PMID:28441135

 

Proteome analysis of human embryonic stem cells organelles

Shekari FNezari HLarijani MRHan CLBaharvand HChen YJSalekdeh GH.

J Proteomics. 2017 Jun 6;162:108-118

PMID: 28435121

 

Landscape of submitochondrial protein distribution.

Vögtle FNBurkhart JMGonczarowska-Jorge HKücükköse CTaskin AAKopczynski DAhrends RMossmann DSickmann AZahedi RPMeisinger C.

Nat Commun. 2017 Aug 18;8(1):290

PMID: 28819139

 

Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale.

Morgenstern MStiller SBLübbert PPeikert CDDannenmaier SDrepper FWeill UHöß PFeuerstein RGebert MBohnert Mvan der Laan MSchuldiner MSchütze COeljeklaus SPfanner NWiedemann NWarscheid 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.

DOWNTIME: Monday 18th of September 2017

MitoMiner will be offline on Monday 18th of September from 09:00 GMT to allow for a major new update. Sorry for any inconvenience. 

DOWNTIME: Saturday 29th of July 2017

MitoMiner will be unavailable from 08:00 GMT Saturday 29th of July until 15:00 GMT. This due to the power supply to the Units servers being upgraded. Sorry for any inconvenience this may cause.

DOWNTIME: Wednesday 7th of June 2017

MitoMiner will be unavailble on Wednesday 7th of June due to server upgrades. Sorry for any inconvenience. 

MitoMiner update coming soon!

In the next few weeks we will be updating all the data in MitoMiner, upgrading the underlying InterMine software and making various bug fixes. If you have any data or feature requests for this upcoming release please contact us at mitominer@mrc-mbu.cam.ac.uk 

MitoMiner Version 4.0 Released!

We have made a significant changes to MitoMiner to produce version 4.0. The most noticeable change is moving from a UniProt protein centric database to a Ensembl Gene centric database. We have also narrowed the focus of the database to 6 organisms: H. sapiens, M. musculus, R. norvegicus, D. rerio, S. cerevisiae, S. pombe. This has significantly reduced redundant entries and has made the database much easier to navigate and search. We have also included many new data types including phenotypes and interaction data. If you have any questions or comments you can write to us at mitominer@mrc-mbu.cam.ac.ukThe old protein centric version is still available and can be found here: http://mitominer.mrc-mbu.cam.ac.uk/release-3.1-archive/  
 
 
Enhancements included for Version 4.0:
 
Zebrafish
We now include annotation and homology data for Zebrafish. 
 
Phenotypes
We include phenotype data from MGI, Zebrafish and S. cerevisiae.
 
Interaction data
We include protein and genetic interaction data from BioGRID for all the species included in MitoMiner.
 
Gene Homology
We have now switched from the NCBI's HomoloGene to Ensembl Compara. 
 
Mitochondrial Targeting Sequences
We now include MitoFates predictions (http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi) as well as iPSORT, MitoProt and TargetP. We also now include cleavage site predictions from MitoFates and MitoProt.
 
Integrated Mitochondrial Protein Index (IMPI) - reference set
MitoMiner now includes an updated IMPI dataset of mitochondrial genes that was created using the new data in MitoMiner 4.0. Further details can be found on the IMPI page: http://mitominer.mrc-mbu.cam.ac.uk/release-4.0-beta/impi.do
 
Many of the other datasources have been refreshed and updated. Further details can be found here: http://mitominer.mrc-mbu.cam.ac.uk/release-4.0-beta/dataCategories.do
 
 
Users of Version 3.1
The new version of MitoMiner uses a new database structure. This was unavoidable and unfortunately means that we are unable to transfer user accounts from the previous version. Therefore existing users will have to set up a new account in v4.0. If you have any queries that you have built in the last version that you would like to use in this new version please contact us. We will be happy to convert them to be compatible with the new database structure.

 

DOWNTIME: Friday 29th April 2016 for upgrade to version 4!

MitoMiner will be offline from 09:00 GMT for approximately 8 hours to allow the deployment of version 4.0! Thank you for your patience and apologies for any inconvenience this may cause.

New MitoMiner publication

We are pleased to announce a new MitoMiner publication in NAR that covers the recent updates to the resource: 

MitoMiner v3.1, an update on the mitochondrial proteomics database. Nucleic Acids Res. 2015 Oct 1. pii: gkv1001. [Epub ahead of print]

Smith, A.C. and Robinson, A.J.

PMID: 26432830 

Pages

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