Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database.

The data model of the signaling pathways database TRANSPATH has been re-engineered to a three-layer model comprising experimental evidences and summarized pathway information, both in a mechanistically detailed manner, and a "semantic" projection for the abstract overview. Each molecule is described in the context of a certain reaction in the multidimensional space of posttranslational modification, molecular family relationships, and the biological species of its origin. The new model makes the data better suitable for reconstructing signaling pathways and networks and mapping expression data, for instance from microarray experiments, onto regulatory networks.

[1]  E. Wingender,et al.  The TGF-β–Smad network: introducing bioinformatic tools , 2002 .

[2]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[3]  Edgar Wingender,et al.  TRANSPATH®: a high quality database focused on signal transduction : Data integration in functional genomics and proteomics: application to biological pathways , 2004 .

[4]  Shoshana J. Wodak,et al.  From Molecular Activities and Processes to Biological Function , 2001, Briefings Bioinform..

[5]  Emek Demir,et al.  PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways , 2002, Bioinform..

[6]  Riichiro Mizoguchi,et al.  Cell Signaling Networks Ontology , 2003, Silico Biol..

[7]  Toshihisa Takagi,et al.  Knowledge representation of signal transduction pathways , 2001, Bioinform..

[8]  H. Lodish,et al.  Positive and negative regulation of type II TGF‐β receptor signal transduction by autophosphorylation on multiple serine residues , 1997, The EMBO journal.

[9]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[10]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[11]  J. Dumont,et al.  Crosstalk and specificity in signalling. Are we crosstalking ourselves into general confusion? , 2001, Cellular signalling.

[12]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[13]  Frank Schacherer,et al.  The TRANSPATH signal transduction database: a knowledge base on signal transduction networks , 2001, Bioinform..

[14]  Sui Huang,et al.  Regulation of Cellular States in Mammalian Cells from a Genomewide View , 2002, Gene Regulations and Metabolism.

[15]  Edgar Wingender,et al.  TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks. , 2004, In silico biology.

[16]  Tsuguchika Kaminuma,et al.  A Pathway Finding System for the Cell Signaling Networks Database , 1998, Silico Biol..

[17]  Tsuguchika Kaminuma,et al.  A Database for Cell Signaling Networks , 1998, J. Comput. Biol..

[18]  Edgar Wingender,et al.  TRANSPATH: An integrated database on signal transduction and a tool for array analysis , 2003, Nucleic Acids Res..

[19]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.