miRNA-lncRNA interaction, lncRNA databases

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microRNAs(miRNAs) and Long noncoding RNAs (lncRNAs) represent the leading edge of cancer research.
Several papers have revealed lncRNA functions by identifying the regulatory relationships between miRNAs and lncRNAs.

There are two related resources for miRNA-lncRNA interactions were listed as follows:
(1) starBase v2.0 is designed for decoding miRNA-lncRNA interaction networks and ceRNA regulatory networks involving lncRNAs and mRNAs from 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.
http://starbase.sysu.edu.cn/

(2) DIANA-LncBase: miRNA-lncRNA interactions from 1 CLIP-Seq datasets and computationally predictions.
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index

There are several lncRNA databases, ChIPBase, lncRNAdb, LNCipedia, NONCODE and NRED.

(1) ChIPBase, ChIPBase is a database for annotating and exploring the expression profiles and the transcriptional regulation of lncRNAs and other ncRNAs..
http://deepbase.sysu.edu.cn/chipbase/

(2) lncRNAdb, contains a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles.
http://www.lncrnadb.org/

(3) LNCipedia: a database for annotated human lncRNA transcript sequences and structures.
http://www.lncipedia.org/

(4) NONCODE, NONCODE provides an integrative annotation of long noncoding RNAs.
http://www.noncode.org/

(5) NRED (ncRNA Expression Database), provides gene expression information for thousands of long ncRNAs in human and mouse. It also contains both microarray and in situ hybridization data, much of which is described here for the first time.
http://jsm-research.imb.uq.edu.au/nred/

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From:

http://www.protocol-online.org/forums/topic/31001-mirna-lncrna-interaction-lncrna-databases/#entry162437

 

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Transcription Factor Binding sites (TFBSs) databases based on ChIP-seq data

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Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:

(1) ChIPBase: a database for transcription factor binding maps and decoding the transcriptional regulation of protein-coding genes, lncRNAs and miRNAs from ChIP-Seq data. release date: 2013 January.
http://deepbase.sysu.edu.cn/chipbase/index.php

(2) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. release date: 2010 Oct.
http://amp.pharm.mssm.edu/lib/chea.jsp

(3) CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. release date: 2012 April.
http://cistrome.dfci.harvard.edu/pc/

(4) CTCFBSDB: a database for CTCF binding sites and genome organization. release date: 2013 January.
http://insulatordb.uthsc.edu

(5) Factorbook: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. release date: 2013 January.
http://www.factorbook.org

(6) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. release date: 2011 March.
http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

(7) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. release date: 2013 January.
http://autosome.ru/HOCOMOCO/

(8) JASPAR 2010: The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. release date: 2010 January.
http://jaspar.genereg.net

(9) SwissRegulon: a database of genome-wide annotations of regulatory sites. release date: 2013 January.
http://swissregulon.unibas.ch/fcgi/sr/swissregulon
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From:

http://www.protocol-online.org/forums/topic/31029-comprehensive-list-of-transcription-factor-binding-site-databases-based-on-chip-seq/

lncRNA databases

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(1) ChIPBase: ChIPBase is a database for annotating and exploring the expression profiles and the transcriptional regulation of lncRNAs and other ncRNAs.
http://deepbase.sysu.edu.cn/chipbase/

(2) lncRNABase: for decoding miRNA-lncRNA(lncRNAs, circRNAs, pseudogenes) and miRNA-ceRNA interaction networks from CLIP-Seq datasets.
http://starbase.sysu.edu.cn/mirLncRNA.php

(3) lncRNAdb: contains a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. website: http://www.lncrnadb.org/

(4) LncRNADisease: a database for long-non-coding RNA-associated diseases.
http://cmbi.bjmu.edu.cn/lncrnadisease

(5) LNCipedia: a database for annotated human lncRNA transcript sequences and structures.
http://www.lncipedia.org

(6) NONCODE: NONCODE provides an integrative annotation of long noncoding RNAs.
http://www.noncode.org

(7) NRED (ncRNA Expression Database):  provides gene expression information for thousands of long ncRNAs in human and mouse. It also contains both microarray and in situ hybridization data, much of which is described here for the first time.
http://jsm-research.imb.uq.edu.au/nred/

(8) PLncDB: Plant Long noncoding RNA Database.
http://chualab.rockefeller.edu/gbrowse2/homepage.html
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From:
http://www.protocol-online.org/forums/topic/31018-comprehensive-list-of-long-noncoding-rnalncrna-resources/