Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set
- Alistair R.R. Forrest1,2,3,7,
- Darrin Taylor1,2,3,
- RIKEN GER Group4,
- GSL Members5,6, and
- Sean Grimmond1,2
- 1The Institute for Molecular Bioscience, University of Queensland, Queensland Q4072, Australia
- 2University of Queensland, Queensland Q4072, Australia
- 3The Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Queensland Q4072, Australia
- 4Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- 5Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
Abstract
The cell cycle is one of the most fundamental processes within a cell. Phase-dependent expression and cell-cycle checkpoints require a high level of control. A large number of genes with varying functions and modes of action are responsible for this biology. In a targeted exploration of the FANTOM2–Variable Protein Set, a number of mouse homologs to known cell-cycle regulators as well as novel members of cell-cycle families were identified. Focusing on two prototype cell-cycle families, the cyclins and the NIMA-related kinases (NEKs), we believe we have identified all of the mouse members of these families, 24 cyclins and 10 NEKs, and mapped them to ENSEMBL transcripts. To attempt to globally identify all potential cell cycle-related genes within mouse, the MGI (Mouse Genome Database) assignments for the RIKEN Representative Set (RPS) and the results from two homology-based queries were merged. We identified 1415 genes with possible cell-cycle roles, and 1758 potential paralogs. We comment on the genes identified in this screen and evaluate the merits of each approach.
Footnotes
-
[Supplemental material is available online at www.genome.org.]
-
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1012403.
-
↵7 Corresponding author. E-MAIL a.forrest{at}imb.uq.edu.au; FAX 61-7-3365-4388.
-
↵6 Takahiro Arakawa, Piero Carninci, Jun Kawai, and Yoshihide Hayashizaki.
-
- Accepted March 31, 2003.
- Received December 3, 2002.
- Cold Spring Harbor Laboratory Press
