DNA repair and chromatin remodeling genes
A list of 177 DNA-repair genes published by Wood RD et al. (Wood RD et al., 2001 and Wood RD et al., 2005) was used, and supplemented with 93 bona fide DNA repair genes identified from literature searches. A gene was defined as a DNA repair gene if it encodes a product that acts directly in the repair process or if it is required for repair by regulating or interacting with other DNA repair gene products during the repair process. A list of DNA remodeling genes was compiled from the literature, as identified by members of the FANTOM consortium (F. Drabløs, Y. Medvedeva, A. Lennartsson, unpublished data).
Data sets
Time series data from six previously published microarray and RNA-seq experiments were downloaded and analyzed. These include one microarray experiment from primary foreskin fribroblasts (Bar-Joseph Z et al., 2008); one microarray experiments from HaCaT keratinocytes (Peña-Diaz J et al., 2013); three microarray experiments from the HeLa (Mjelle et al., 2014, Peña-Diaz J et al., 2013 and Whitfield ML et al., 2002); and one RNA-Seq experiment from HeLa (Stumpf et al., 2013). We also included one data set on ribosomal profiling that gives information on translation regulation in the cell cycle.
Data analysis
Cell cycle regulated genes were identified using partial least square (PLS) regression on to a sine and cosine function. Each gene was assigned a cell cycle phase as described in detail by Peña-Diaz J et al. (Peña-Diaz J et al., 2013). The RNA-seq data from Stumpf et al. (Stumpf et al., 2013) was analysed by a standard limma approach in R, comparing each cell phase and detecting significant up-regulated genes.
Links to original data
Refrences
R.D. Wood, M. Mitchell, T. Lindahl, Human DNA repair genes, 2005, Mutat. Res., 577 (2005) 275-283.
R.D. Wood, M. Mitchell, J. Sgouros, T. Lindahl, Human DNA repair genes, Science, 291 (2001) 1284-1289.
J. Pena-Diaz, S.A. Hegre, E. Anderssen, P.A. Aas, R. Mjelle, G.D. Gilfillan, R. Lyle, F. Drablos, H.E. Krokan, P. Saetrom, Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication, Nucl. Acid Res., 41 (2013) 2846-2856.
C.R. Stumpf, M.V. Moreno, A.B. Olshen, B.S. Taylor, D. Ruggero, The translational landscape of the mammalian cell cycle, Mol. Cell, 52 (2013) 574-582.
Z. Bar-Joseph, Z. Siegfried, M. Brandeis, B. Brors, Y. Lu, R. Eils, B.D. Dynlacht, I. Simon, Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells, Proc. Natl. Acad. Sci. U.S.A., 105 (2008) 955-960.
Mjelle et al., Current article (2014)