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| Title: | Cataloguing proteins in cell cycle control |
| Author: | Kazimierez O Wrzeszczynski & Burkhard Rost |
| Quote: | 2003 In Cell Cycle Checkpoint Control Protocols, H Lieberman (ed.), Totowa: Humana Press, 219-233 |
Bioinformatics makes a number of methods available that can also be used to identify cell cycle related proteins. Nevertheless, few tools are specifically designed to cope with cell cycle proteins. In fact, a vast amount of data is currently scattered among many databases. Here, we present a first detailed analysis of known cell cycle proteins. We combined databases mining and literature searches with an evaluation of evolutionary conservation. The objective was to identify cell cycle control proteins in various proteomes. In total we found 595 experimentally annotated cell cycle control proteins; these clustered into 113 distinct structural families. We noticed that neither simple values for pairwise sequence identity nor expectation values taken from popular PSI-BLAST alignments allow an error-free inference of involvement in cell cycle control by sequence similarity. However, when we also considered alignment length we could find thresholds for reliable inference of cell cycle proteins. Applying these safe thresholds to the six entirely sequenced organisms (human, mouse, fly, worm, arabidopsis and yeast), we could identify 463 un-annotated proteins likely to be involved in cell cycle control. Slightly lower levels of accuracy extended the count to approximately 500-1300 additional proteins, which may be candidates for involvement in cell cycle control process.