Table 1.

Databases and softwares used in this study.

Application	Program/database	Reference/address
Finding mRNA isoforms	Ace view	www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
	UCSC	http://genome.ucsc.edu/
Expression analysis	Ace view	www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
	Affymetrix exon array GNF Gene Expression Atlas2	http://genome.ucsc.edu/
Promoter detection	Hidden Markov Model	UCSC (http://genome.ucsc.edu/)
	CoreBoost_HM Promoter Prediction	UCSC (http://genome.ucsc.edu/)
	Promoter scan	www-bimas.cit.nih.gov/molbio/proscan/
	Promoter2	www.cbs.dtu.dk/services/Promoter
Alternative transcription start sites	DBTSS	http://dbtss.hgc.jp/
	Eponine	UCSC (http://genome.ucsc.edu/)
	SwithGear	UCSC (http://genome.ucsc.edu/)
Detection of CpGIs	UCSC	http://genome.ucsc.edu/
	Bona fide CGIs	http://epigraph.mpi-inf.mpg.de/download/CpG_islands_revisited/
	CpGProD	http://pbil.univ-lyon1.fr/software/cpgprod.html
	CpGcluster	http://bioinfo2.ugr.es/CpGcluster/
	CpG-MI tool	http://bioinfo.hrbmu.edu.cn/cpgmi/
	Weizmann Evolutionary CpG Islands	UCSC (http://genome.ucsc.edu/)
Estimation of the CGI's methylation status	Bona fide CGIs	http://epigraph.mpi-inf.mpg.de/download/CpG_islands_revisited/
Finding repeated sequences	Estimation of repeat variability	http://hulsweb1.cgr.harvard.edu/SERV/
	Repeat masker	http://genome.ucsc.edu/
Inspecting histone marks	UCSC	http://genome.ucsc.edu/
DNase I hypersensitive sites	UCSC	http://genome.ucsc.edu/
Transcription factor binding sites	CisRed	www.cisred.org/
	PReMode	http://genomequebec.mcgill.ca/PReMod/
	ENCODE	UCSC (http://genome.ucsc.edu/)
Prediction of insulator sites	CTCFBSDB	http://insulatordb.uthsc.edu