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LOCATE: a mammalian protein subcellular localization database.

Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD - Nucleic Acids Res. (2007)

Bottom Line: Over the past 2 years, the data in LOCATE have grown substantially.Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data.Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

ABSTRACT
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data. Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. It is available at http://locate.imb.uq.edu.au/

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Organelle proteomics—defining the protein complement of individual organelles.
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Figure 2: Organelle proteomics—defining the protein complement of individual organelles.

Mentions: One of the key objectives of this database is to provide the protein content of a particular region of the cell, termed Location Proteome (13). Figure 2 shows the location proteomes of the major cellular compartments. We have compared the data collected from other sources with our independently annotated primary literature subcellular localization data from LOCATE. The cytoplasm (29.3% other; 6.9% primary) has been excluded as it contained limited representation in our annotations and proteins remaining at their site of biosynthesis do not represent an active transport event. Within these estimates each TU contributes equally and when multiple subcellular compartments were annotated each annotation was proportionally distributed. The differences between the two subcellular localization datasets have been discussed previously (11). Our primary localization annotations are based exclusively on experimental data and aim to represent the predominant subcellular localization. It does not well represent proteins that have multiple cellular localizations in the same cell or across distinct cell types and those induced into trafficking pathways by activation of cellular pathways. In contrast, the other subcellular localization dataset captures any subcellular localization without considering the relative distributions across multiple localization or the source of the annotation. Within the primary data set the largest compartment proteomes are the nuclear proteome with 38% of the proteins and the extracellular/plasma membrane proteome with 31% of the proteins. The other intracellular organelles proteomes are of a similar size mitochondria proteome 6.2%; endoplasmic reticulum proteome 7.0%; Golgi Apparatus proteome 7.1% and endosome/lysosome 5.8%. Within the other subcellular localisation data the mitochondria proteome, endoplasmic reticulum proteome and cytoskeleton proteome have higher estimates. The list of proteins within each region is accessible from the LOCATE homepage.Figure 2.


LOCATE: a mammalian protein subcellular localization database.

Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD - Nucleic Acids Res. (2007)

Organelle proteomics—defining the protein complement of individual organelles.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238969&req=5

Figure 2: Organelle proteomics—defining the protein complement of individual organelles.
Mentions: One of the key objectives of this database is to provide the protein content of a particular region of the cell, termed Location Proteome (13). Figure 2 shows the location proteomes of the major cellular compartments. We have compared the data collected from other sources with our independently annotated primary literature subcellular localization data from LOCATE. The cytoplasm (29.3% other; 6.9% primary) has been excluded as it contained limited representation in our annotations and proteins remaining at their site of biosynthesis do not represent an active transport event. Within these estimates each TU contributes equally and when multiple subcellular compartments were annotated each annotation was proportionally distributed. The differences between the two subcellular localization datasets have been discussed previously (11). Our primary localization annotations are based exclusively on experimental data and aim to represent the predominant subcellular localization. It does not well represent proteins that have multiple cellular localizations in the same cell or across distinct cell types and those induced into trafficking pathways by activation of cellular pathways. In contrast, the other subcellular localization dataset captures any subcellular localization without considering the relative distributions across multiple localization or the source of the annotation. Within the primary data set the largest compartment proteomes are the nuclear proteome with 38% of the proteins and the extracellular/plasma membrane proteome with 31% of the proteins. The other intracellular organelles proteomes are of a similar size mitochondria proteome 6.2%; endoplasmic reticulum proteome 7.0%; Golgi Apparatus proteome 7.1% and endosome/lysosome 5.8%. Within the other subcellular localisation data the mitochondria proteome, endoplasmic reticulum proteome and cytoskeleton proteome have higher estimates. The list of proteins within each region is accessible from the LOCATE homepage.Figure 2.

Bottom Line: Over the past 2 years, the data in LOCATE have grown substantially.Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data.Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

ABSTRACT
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data. Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. It is available at http://locate.imb.uq.edu.au/

Show MeSH