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Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set
Alistair R R Forrest1, Darrin Taylor, Sean Grimmond
1The Institute for Molecular Bioscience, University of Queensland, Queensland Q4072, Australia. a.forrest@imb.uq.edu.au
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.
Insights
Researchers identified mouse cell cycle genes, including 24 cyclins and 10 NIMA-related kinases (NEKs). This study cataloged 1415 potential cell cycle genes and 1758 paralogs in mice.
Area of Science:
- Molecular Biology
- Genomics
- Cellular Biology
Background:
- The cell cycle is a fundamental cellular process requiring precise regulation.
- Phase-dependent gene expression and checkpoints necessitate intricate control mechanisms.
- Numerous genes with diverse functions govern cell cycle biology.
Purpose of the Study:
- To identify mouse homologs of known cell cycle regulators and novel members.
- To comprehensively catalog mouse cell cycle-associated genes.
- To map identified genes to ENSEMBL transcripts for further analysis.
Main Methods:
- Targeted exploration of the FANTOM2-Variable Protein Set.
- Focused analysis of cyclin and NIMA-related kinase (NEK) families.
- Integration of MGI assignments and homology-based queries for global gene identification.
Main Results:
- Identified 24 mouse cyclins and 10 mouse NEKs, mapping them to ENSEMBL transcripts.
- Discovered 1415 genes with potential cell cycle roles.
- Found 1758 potential paralogs of cell cycle-related genes.
Conclusions:
- The study successfully identified and cataloged a significant number of mouse cell cycle genes.
- The comprehensive approach provides a valuable resource for cell cycle research.
- Further investigation into the identified genes can elucidate novel regulatory mechanisms.