Open Access Highly Accessed Database

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease

Satoshi Mizuno1, Risa Iijima1, Soichi Ogishima1*, Masataka Kikuchi1, Yukiko Matsuoka23, Samik Ghosh2, Tadashi Miyamoto1, Akinori Miyashita4, Ryozo Kuwano4 and Hiroshi Tanaka1

Author Affiliations

1 Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8510, Japan

2 Systems Biology Institute, Shirokanedai 5-6-9, Minato-ku, Tokyo, 108-0071, Japan

3 JST ERATO Kawaoka Infection-induced Host Response Network Project, The Institute of Medical Science, University of Tokyo, Bld 2, 4F, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan

4 Department of Molecular Genetics, Center for Bioresources, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan

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BMC Systems Biology 2012, 6:52  doi:10.1186/1752-0509-6-52

Published: 30 May 2012

Additional files

Additional file 1::

SBML map file of AlzPathway. The SBML map file alzpathway_sbml_map.xml can be browsed using CellDesigner. Please download CellDesigner at http://www.celldesigner.org/ webcite, install it, and open the SBML map file alzpathway_sbml_map.xml to browse AlzPathway map by CellDesigner. As for usage of CellDesigner software, see the documentations provided at CellDesigner web site: http://www.celldesigner.org/documents.html. webcite

Format: XML Size: 6.2MB Download file

Open Data

Additional file 2::

High resolution image map of AlzPathway. The PNG file alzpathway_image_map.png contains a high resolution map of AlzPathway. This image map does not contain the reference information used for constructing the AlzPathway. SBML (CellDesigner) map and Online map (Payao) are recommended to browse the AlzPathway map.

Format: PNG Size: 8.4MB Download file

Open Data

Additional file 3::

Instruction on usage of Payao. The PDF file alzpathway_payao_access_instruction.pdf contains insturction on usage of Payao web service (online map). Payao system requires login. AlzPathway demo user account is prepared for demo use: demo username is “ap_demo” and the corresponding password is “4patients”. As for usage of Payao system, see the user’s guide provided at Payao web site: http://payao.oist.jp:8080/payaologue/doc/PAYAO_Users_GuideE11.pdf. webcite

Format: PDF Size: 653KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4::

Binary-relation notation file of AlzPathway. The SIF (simple interaction format) file alzpathway_binary_relation.sif is the binary-relation notation of AlzPathway map which can be opened by using Cytoscape.

Format: SIF Size: 38KB Download file

Open Data

Additional file 5::

Pure SBML map file of AlzPathway. The pure SBML file alzpathway_pure_sbml.xml is for compatibility with other SMBL supporting tools.

Format: XML Size: 1.5MB Download file

Open Data

Additional file 6::

BioPAX file of AlzPathway. The BioPAX file alzpathway_biopax.owl is for exchanges of pathway data.

Format: OWL Size: 2.2MB Download file

Open Data

Additional file 7::

Expanded SBML map file of AlzPathway with Gene Ontology. The SBML map file alzpathway_sbml_map_go.xml is the expanded version of AlzPathway map (alzpathway_sbml_map.xml) having external links to Gene Ontology. The SBML map file with the external links to Gene Ontology requires time to be opened by CellDesigner 4.2, and thus was provided separately as an expanded SBML map.

Format: XML Size: 14.1MB Download file

Open Data