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. 2010 Jul;38(Web Server issue):W124-31.
doi: 10.1093/nar/gkq499. Epub 2010 Jun 10.

PINT: Pathways INtegration Tool

Y-T Wang  1 , Y-H Huang, Y-C Chen, C-L Hsu, U-C Yang
Affiliations

PINT: Pathways INtegration Tool

Y-T Wang et al. Nucleic Acids Res. 2010 Jul.

Abstract

New pathway databases generally display pathways by retrieving information from a database dynamically. Some of them even provide their pathways in SBML or other exchangeable formats. Integrating these models is a challenging work, because these models were not built in the same way. Pathways integration Tool (PINT) may integrate the standard SBML files. Since these files may be obtained from different sources, any inconsistency in component names can be revised by using an annotation editor upon uploading a pathway model. This integration function greatly simplifies the building of a complex model from small models. To get new users started, about 190 curated public models of human pathways were collected by PINT. Relevant models can be selected and sent to the workbench by using a user-friendly query interface, which also accepts a gene list derived from high-throughput experiments. The models on the workbench, from either a public or a private source, can be integrated and painted. The painting function is useful for highlighting important genes or even their expression level on a merged pathway diagram, so that the biological significance can be revealed. This tool is freely available at http://csb2.ym.edu.tw/pint/.

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Figures

Figure 1.
Figure 1.
The PINT pathways-integration process. (A) and (B) are the general rules with which PINT performs pathways-integration process. (C) is a process diagram and (D) is an entity relationship diagram, where both are considered to be equivalent by PINT.
Figure 2.
Figure 2.
System flow of PINT. *Users can re-upload the SBML file exported from PINT. **PINT will accept the SBML files generated by SBMLeditor. 1A gene list and fold change file should follow a particular format (Supplementary Figures S11 and S13). 2Tissue information was retrieved from UniGene (Build 221) (http://www.ncbi.nlm.nih.gov/unigene).
See this image and copyright information in PMC

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