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The Molecule Pages database.

Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I - Nucleic Acids Res. (2007)

Bottom Line: The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function.The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer.The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center San Diego, La Jolla, CA 92093, Nature Publishing Group, 25 First Street, Cambridge, MA 02141, USA.

ABSTRACT
The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

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Domain/Motif map for Syk (A000040).
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Figure 4: Domain/Motif map for Syk (A000040).

Mentions: The ‘Protein Records’ section displays all the sequence database records related to particular Molecule Page. A specific record, defined by an NCBI protein GI number (3), is assigned to the Molecule Page as a base sequence. All the other sequence records listed in the same Entrez Gene (4) record are displayed, as well as any UniProt (5) and Ensembl (6) records that refer to those sequence records. The records are grouped by their specific sequence. The ‘Gene Info’ page displays pertinent information related to the Molecule from the Entrez Gene record, including any related Ensembl gene records or the sequence records within it. The ‘Domains & Motifs’ (Figure 4) section contains domain information Pfam (7) and Smart (8), pattern/motif information from PRINTS (9) and InterPRO (10) records related to the Molecule Page sequence. These records are produced using a combination of database record references, computational schemes [hmmpfam (11) and FingerPRINTScan (12)]. Matching sequence regions are given for the computational matches. The ‘Interactions’ page displays matching interaction database records from the BIND database and from the Entrez Gene database, including BIND (13), BioGRID (14) and HPRD (15) interaction records. Interactions involving likely orthologs of the Molecule Page base sequence are displayed, to provide additional information. The ‘Orthologs’ section shows genes in other select organisms that are likely orthologs of the base gene. This list is constructed using a combination of a species-specific Blast against the NCBI protein database, and database analysis of HomoloGene (16) and Ensembl homology databases. The ‘Blast Data’ section contains a list of the top Blast hits against the entire NCBI protein database. The Protein ‘Structure’ section displays the PDB (17) records that are related to the Molecule Page, either through a database reference to one of the related protein sequence records, or by a sequence match with Blast.Figure 4.


The Molecule Pages database.

Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I - Nucleic Acids Res. (2007)

Domain/Motif map for Syk (A000040).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238911&req=5

Figure 4: Domain/Motif map for Syk (A000040).
Mentions: The ‘Protein Records’ section displays all the sequence database records related to particular Molecule Page. A specific record, defined by an NCBI protein GI number (3), is assigned to the Molecule Page as a base sequence. All the other sequence records listed in the same Entrez Gene (4) record are displayed, as well as any UniProt (5) and Ensembl (6) records that refer to those sequence records. The records are grouped by their specific sequence. The ‘Gene Info’ page displays pertinent information related to the Molecule from the Entrez Gene record, including any related Ensembl gene records or the sequence records within it. The ‘Domains & Motifs’ (Figure 4) section contains domain information Pfam (7) and Smart (8), pattern/motif information from PRINTS (9) and InterPRO (10) records related to the Molecule Page sequence. These records are produced using a combination of database record references, computational schemes [hmmpfam (11) and FingerPRINTScan (12)]. Matching sequence regions are given for the computational matches. The ‘Interactions’ page displays matching interaction database records from the BIND database and from the Entrez Gene database, including BIND (13), BioGRID (14) and HPRD (15) interaction records. Interactions involving likely orthologs of the Molecule Page base sequence are displayed, to provide additional information. The ‘Orthologs’ section shows genes in other select organisms that are likely orthologs of the base gene. This list is constructed using a combination of a species-specific Blast against the NCBI protein database, and database analysis of HomoloGene (16) and Ensembl homology databases. The ‘Blast Data’ section contains a list of the top Blast hits against the entire NCBI protein database. The Protein ‘Structure’ section displays the PDB (17) records that are related to the Molecule Page, either through a database reference to one of the related protein sequence records, or by a sequence match with Blast.Figure 4.

Bottom Line: The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function.The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer.The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center San Diego, La Jolla, CA 92093, Nature Publishing Group, 25 First Street, Cambridge, MA 02141, USA.

ABSTRACT
The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

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