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PaxDb, a database of protein abundance averages across all three domains of life.

Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C - Mol. Cell Proteomics (2012)

Bottom Line: Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels.Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline.We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

ABSTRACT
Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels. These extend from a few molecules per cell for signaling proteins, to millions of molecules for structural proteins. When addressing fundamental questions related to protein evolution, translation and folding, but also in routine laboratory work, a simple rough estimate of the average wild type abundance of each detectable protein in an organism is often desirable. Here, we introduce a meta-resource dedicated to integrating information on absolute protein abundance levels; we place particular emphasis on deep coverage, consistent post-processing and comparability across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over the various samples, conditions and cell-types, the resulting integrated data set achieves increased coverage and a high dynamic range. We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually. The current PaxDb-release 2.1 (at http://pax-db.org/) presents whole-organism data as well as tissue-resolved data, and covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across organisms via pre-computed orthology relationships.

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Related in: MedlinePlus

The organism page. This page provides general information about the selected organism, such as the number of data sets and the proteome coverage; it also provides a histogram showing the distribution of protein abundances in the “integrated” data set. The bottom panel lists all available data sets for the selected species. On each page in PaxDb, the very top panel contains a search box that allows the user to search for both protein names and annotations.
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Figure 3: The organism page. This page provides general information about the selected organism, such as the number of data sets and the proteome coverage; it also provides a histogram showing the distribution of protein abundances in the “integrated” data set. The bottom panel lists all available data sets for the selected species. On each page in PaxDb, the very top panel contains a search box that allows the user to search for both protein names and annotations.

Mentions: The website of PaxDb (Figs. 3 and 4; and http://pax-db.org/) has been designed for intuitive and fast access, allowing both the ad-hoc query of a protein family of interest, as well as browsing and comparing entire data sets. Protein queries are resolved against a large collection of identifier name-spaces, and multiple proteins can be requested simultaneously in one query. In addition to searching for known identifiers, the user queries are also searched against the annotations of all proteins in PaxDb, using a fast full-text search. For each organism in PaxDb, a distinct summary page provides information on data provenance, its coverage and estimated quality (Fig. 3). This page also provides the distribution of abundance values of each data set as a histogram, as well as listing the most abundant proteins in the organism. Users can open and browse entire data sets from this page, and from these data set tables they can proceed directly to the protein details page and, in the case of PeptideAtlas data, also directly back to the underlying peptide information via deep links.


PaxDb, a database of protein abundance averages across all three domains of life.

Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C - Mol. Cell Proteomics (2012)

The organism page. This page provides general information about the selected organism, such as the number of data sets and the proteome coverage; it also provides a histogram showing the distribution of protein abundances in the “integrated” data set. The bottom panel lists all available data sets for the selected species. On each page in PaxDb, the very top panel contains a search box that allows the user to search for both protein names and annotations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3412977&req=5

Figure 3: The organism page. This page provides general information about the selected organism, such as the number of data sets and the proteome coverage; it also provides a histogram showing the distribution of protein abundances in the “integrated” data set. The bottom panel lists all available data sets for the selected species. On each page in PaxDb, the very top panel contains a search box that allows the user to search for both protein names and annotations.
Mentions: The website of PaxDb (Figs. 3 and 4; and http://pax-db.org/) has been designed for intuitive and fast access, allowing both the ad-hoc query of a protein family of interest, as well as browsing and comparing entire data sets. Protein queries are resolved against a large collection of identifier name-spaces, and multiple proteins can be requested simultaneously in one query. In addition to searching for known identifiers, the user queries are also searched against the annotations of all proteins in PaxDb, using a fast full-text search. For each organism in PaxDb, a distinct summary page provides information on data provenance, its coverage and estimated quality (Fig. 3). This page also provides the distribution of abundance values of each data set as a histogram, as well as listing the most abundant proteins in the organism. Users can open and browse entire data sets from this page, and from these data set tables they can proceed directly to the protein details page and, in the case of PeptideAtlas data, also directly back to the underlying peptide information via deep links.

Bottom Line: Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels.Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline.We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

ABSTRACT
Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels. These extend from a few molecules per cell for signaling proteins, to millions of molecules for structural proteins. When addressing fundamental questions related to protein evolution, translation and folding, but also in routine laboratory work, a simple rough estimate of the average wild type abundance of each detectable protein in an organism is often desirable. Here, we introduce a meta-resource dedicated to integrating information on absolute protein abundance levels; we place particular emphasis on deep coverage, consistent post-processing and comparability across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over the various samples, conditions and cell-types, the resulting integrated data set achieves increased coverage and a high dynamic range. We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually. The current PaxDb-release 2.1 (at http://pax-db.org/) presents whole-organism data as well as tissue-resolved data, and covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across organisms via pre-computed orthology relationships.

Show MeSH
Related in: MedlinePlus