ContDist: a tool for the analysis of quantitative gene and promoter properties

Hackenberg, Michael; Lasso, Gorka; Matthiesen, Rune

doi:10.1186/1471-2105-10-7

BMC Bioinformatics

Table 2 A summary of the comparison of unmethylated and differentially methylated promoters.

From: ContDist: a tool for the analysis of quantitative gene and promoter properties

	UnM		Differentially M
Feature	Mean	Median	Mean	Median	p-value_KS	p-value_Rand
G+C in R3	*64.50*	*64.34*	*57.07*	*57.11*	*2.13E-05*	*1.00E-04*
G+C in R6	50.04	49.87	49.02	47.87	4.70E-01	0.3731
G+C in introns	47.31	47.3	49.55	49.58	6.35E-01	0.1699
G+C in 3' UTR	45.8	46.29	47.17	48.47	5.67E-01	0.4603
G+C in 3 position	60.91	63.42	64.37	69.08	3.10E-01	0.2065
CA density in R3	*0.0523*	*0.05*	*0.06493*	*0.065*	*3.37E-05*	*1.00E-04*
CG density in R3	*0.08597*	*0.085*	*0.04297*	*0.0375*	*1.53E-09*	*1.00E-04*
TG density in R3	*0.06039*	*0.06*	*0.07723*	*0.0775*	*3.31E-06*	*1.00E-04*
Twist in R3	*0.02515*	*0.02518*	*0.02564*	*0.0257*	*4.91E-10*	*1.00E-04*
Tilt in R3	0.03556	0.03556	0.03546	0.03548	3.29E-01	0.1409
Rise in R3	*7.82035*	*7.82304*	*7.79215*	*7.79555*	*2.79E-07*	*1.00E-04*
Roll in R3	*0.01984*	*0.01984*	*0.01979*	*0.01979*	*3.19E-04*	*1.00E-04*
Shift in R3	*1.31184*	*1.31192*	*1.32067*	*1.32122*	*3.08E-03*	*0.0004*
Slide in R3	*2.09794*	*2.09697*	*2.11725*	*2.1185*	*1.16E-02*	*0.0014*
Bock-comb in R1	*0.59871*	*0.5875*	*0.43191*	*0.415*	*5.67E-05*	*1.00E-04*
unMeth prob in R3	*0.65596*	*0.79195*	*0.3217*	*0.20742*	*4.26E-08*	*1.00E-04*
Ka/Ks hsa/mmu	*0.10729*	*0.08677*	*0.20001*	*0.15901*	*8.09E-04*	*0.0003*
nucC hsa/mmu	*0.14416*	*0.13743*	*0.21186*	*0.19773*	*1.68E-05*	*1.00E-04*
protC hsa/mmu	*0.11891*	*0.09942*	*0.24044*	*0.22569*	*4.63E-05*	*1.00E-04*
Nc	48.29	49.26	47.03	47.82	6.38E-01	0.3138
peakExpression	3727	1392	2966	1403	6.77E-01	0.6982
Expression Breadth	*66.00*	*81.65*	*51.30*	*50.63*	*4.07E-02*	*0.0234*

Significant differences are highlighted in bold. "R" is used to specify different promoter regions: R1 is the Transcription Start Site (TSS), R3 [TSS -200 bp; TSS + 200 bp] and R6 [TSS -1500 bp; TSS]. G+C stands for the GC-content, Bock-comb is the combinatorial score (see http://epigraph.mpi-inf.mpg.de/download/CpG_islands_revisited/) of Bock CpG islands overlapping the TSS (R1 regions) and "unMeth prob in R3" is the mean probability of the R3 region to remain unmethylated. nucC and protC are the substitution probabilities per base/amino acid (hsa/mmu indicates that the values are based on pair wise alignments between human and mouse) and Nc is the codon bias. M is the abbreviation of "methylated".

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com