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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

A multi-factor model for caspase degradome prediction

Lawrence JK Wee12, Joo Chuan Tong3, Tin Wee Tan1 and Shoba Ranganathan14*

Author Affiliations

1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

2 Singapore Immunology Network, Singapore

3 Institute for Infocomm Research, 1 Fusionpolis Way, #21-01 Connexis, Singapore 138632

4 Department of Chemistry and Biomolecular Sciences & ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia

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BMC Genomics 2009, 10(Suppl 3):S6  doi:10.1186/1471-2164-10-S3-S6

Published: 3 December 2009

Additional files

Additional file 1:

Matrix showing global mapping of reported caspase cleavage sites across all known substrates. Each cell in table shows the frequency of occurrence of an experimentally verified caspase cleavage site sequence (column) in a known substrate (row). Coloured cell indicates frequency of occurrence of that sequence in the substrate (yellow, 1; orange, 2; red, 3 and above).

Format: XLS Size: 262KB Download file

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Open Data

Additional file 2:

Global mapping of predicted caspase cleavage sites on receptor tyrosine kinases. Positions of CASVM predicted cleavage sites on protein sequence of each RTK member are listed. Numbers indicate the positions of P1 (Asp) residues on protein sequences. All cleavage site positions are color coded; grey indicates location of cleavage site within the extracellular domain, blue indicates location within intracellular domain and darker blue indicates location within kinase domain (all kinase domains of RTKs are located in the intracellular domain of the receptor). Predicted cleavage sites corresponding to true experimentally verified cleavage sites on EGFR, ERBB2, MET, ALK and RET are underlined. Yellow highlights indicate predicted cleavage sites with P-score of 0.3 or smaller.

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Open Data

Additional file 3:

Analysis dataset of caspase substrate cleavage sites. List of caspase substrate cleavage sites used for the analysis of structural features and for the optimization of the prediction model parameters. Cleavage sites are reported as tetrapeptides in the order: P4-P3-P2-P1. All cleavage sites have an Asp (D) in the P1 position. The position of the P1 amino acid in the protein sequence is given as reported in Uniprot.

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Open Data

Additional file 4:

Optimization of α and β coefficients in the P-score function. Pools of cleavage site subsequences (74) and non-cleavage site subsequences (74) were assigned with P-score values using different combinations of α and β coefficient values (1.0 to 0.0 and 0.0 to 1.0 respectively). The two pools were measured for the fraction of subsequences (vertical axis) with scores above the P-score cut-offs (horizontal axis) (blue line: cleavage site subsequences, red line: non-cleavage site subsequences, green line: all subsequences) using the different combinations of α and β coefficients (Figures A-K). The values of 0.3 and 0.7 were selected for α and β coefficients respectively as the resultant P-score function produced the best combination of cleavage site subsequences retention and elimination of non-cleavage site subsequences under increasing P-score cut-offs.

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Open Data