Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling)

BMC Bioinformatics

Table 1 Circadian effect for 9 genes put forward in the Hazen study

Gene ID	Name	Overlap	Max. Eff.	Top 20
AT1G22770	GIGANTEA	0.529	2.28	yes
AT1G68050	FLAVIN-BINDING KELCH DFB PROTEIN1	0.867	2.90	yes
AT2G25930	EARLY FLOWERING3	0.562	1.46	yes
AT2G46790	PSEUDO RESPONSE REGULATOR9	0.473	1.38	yes
AT2G46830	CIRCADIAN CLOCK ASSOCIATED1	0.867	3.89	yes
AT3G22380	TIME FOR COFFEE	0.040	0.06	no
AT3G46640	LUX ARRHYTHMO	0.717	1.69	yes
AT5G57360	ZEITLUPE	0.350	0.41	no
AT5G61380	TIMING OF CAB2 EXPRESSION1	0.797	1.74	yes

Analysis results for 8 circadian clock associated genes and for TIME FOR COFFEE, a clock gene that does not cycle at the transcriptional level. These are the genes on the forward strand that were also tested in [13]. Overlap indicates the proportion of overlap between the regions detected by the wavelet-based method and the gene annotation; Max. Eff. gives the maximum estimated effect or amplitude size for this gene; Top 20 indicates whether the gene is within the top 20 genes with the strongest circadian effect for the associated chromosome, as produced by the wavelet-based method.

ISSN: 1471-2105