Infrastructures of systems biology that facilitate functional genomic study in rice

Hong, Woo-Jong; Kim, Yu-Jin; Chandran, Anil Kumar Nalini; Jung, Ki-Hong

doi:10.1186/s12284-019-0276-z

Rice

Table 2 List of databases for rice transcriptomics

From: Infrastructures of systems biology that facilitate functional genomic study in rice

Category	Database	Resource link	Reference	Status	Citation/since
Expression profile	EXPath 2.0	http://expath.itps.ncku.edu.tw/	10.1186/1471-2164-16-S2-S6	○ ^a	11/2015
	PLEXdb	http://www.plexdb.org/index.php	10.1093/nar/gkr938	○	231/2012
	Rice eFP browser	http://bar.utoronto.ca/efprice/cgi-bin/efpWeb.cgi	10.1111/j.1365-313X.2012.05055.x	○	61/2012
	RiceXPro	http://ricexpro.dna.affrc.go.jp/	10.1093/nar/gks1125	○	166/2011
	RED	http://expression.ic4r.org/	10.1016/j.jgg.2017.05.003	○	6/2017
	TENOR	https://tenor.dna.affrc.go.jp/	10.1093/pcp/pcv179	○	31/2016
	OryzaExpress	http://plantomics.mind.meiji.ac.jp/OryzaExpress/	10.1093/pcp/pcq195	○	81/2011
	UniVIO	http://univio.psc.riken.jp/	10.1093/pcp/pct003	○	24/2013
	Genevestigator	https://genevestigator.com/gv/doc/intro_plant.jsp	10.1155/2008/420747	○	2476/2004
	Expression Atlas	https://www.ebi.ac.uk/gxa/experiments?organism=Oryza+sativa+Japonica+Group	10.1093/nar/gkv1045	○	192/2009
	CREP	http://crep.ncpgr.cn/crep-cgi/home.pl	10.1111/j.1365-313X.2009.04100.x	○	240/2010
Non coding RNA	PlantRNA	http://plantrna.ibmp.cnrs.fr/plantrna/	10.1093/nar/gks935	○	33/2012
	CSRDB	http://sundarlab.ucdavis.edu/smrnas/	10.1093/nar/gkl991	○	101/2007
	PNRD	http://structuralbiology.cau.edu.cn/PNRD/index.php	10.1093/nar/gku1162	○	72/2014
	IsomiR Bank	https://mcg.ustc.edu.cn/bsc/isomir/	10.1093/bioinformatics/btw070	○	15/2016
	miRBase	http://www.mirbase.org/	10.1093/nar/gkt1181	○	4106/2006
	PceRBase	http://bis.zju.edu.cn/pcernadb/index.jsp	10.1093/nar/gkw916	○	15/2017
	PlantcircBase	http://ibi.zju.edu.cn/plantcircbase/	10.1016/j.molp.2017.03.003	○	24/2017
	Plant rDNA database	http://www.plantrdnadatabase.com/	10.1007/s00412-012-0368-7	○	47/2012
	lncrnadb	http://www.lncrnadb.org/	10.1093/nar/gkq1138	○	452/2010
	GreeNC	http://greenc.sciencedesigners.com/wiki/Main_Page	10.1093/nar/gkv1215	○	29/2015
Co-expression analysis	PLANEX	http://planex.plantbioinformatics.org/	10.1186/1471-2229-13-83	○	25/2013
	ATTED-II	http://atted.jp/	10.1093/pcp/pcx191	○	371/2007
	PODC	http://plantomics.mind.meiji.ac.jp/podc/	10.1093/pcp/pcu188	○	32/2015
	COP DB	http://webs2.kazusa.or.jp/kagiana/cop0911/	10.1093/bioinformatics/btq121	○	66/2010
	PlantArrayNet	http://bioinfo.mju.ac.kr/arraynet/	10.1104/pp.109.139030	○	82/2009
	RiceFREND	http://ricefrend.dna.affrc.go.jp/publication.html	10.1093/nar/gks1122	○	64/2013
	NetMiner	https://github.com/czllab/NetMiner	10.1371/journal.pone.0192613	○	2/2018
Promoter analysis	PlantPAN_V2	http://plantpan2.itps.ncku.edu.tw/index.html	10.1093/nar/gkv1035	○	263/2008
	PPDB	http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi	10.1093/nar/gkt1027	○	47/2007
	PlantCARE	http://bioinformatics.psb.ugent.be/webtools/plantcare/html/	10.1093/nar/30.1.325	○	1801/2002
	PLACE	https://sogo.dna.affrc.go.jp/cgi-bin/sogo.cgi?lang=en&pj=640&action=page&page=newplace	10.1093/nar/27.1.297	○	2818/2007

^aindicates that relating data is currently working

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