Resources

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Databases (C. elegans)[edit]

3' UTRome

AcePrimer (C. elegans)

AceView (C. elegans)

Caenorhabditis Genetics Center (CGC)

C. elegans gene knockouts (consortium)

C. elegans gene knockouts (National Bioresource Project for the Experimental Animal "Nematode C. elegans" Japan)

Expression patters for C. elegans promoter::GFP fusions

Mitani C. elegans Deletion Strains

Nematode Expression Pattern DataBase (NEXTDB aka Kohara dataset)

Textpresso (C. elegans)

TransgenOme

The Worm Breeder's Gazette

Worm ORFeome

WormAtlas

WormBase

WormBook

The WormImage Database 

Databases (Other)[edit]

The Coli Genetic Stock Center

FlyBase

Interactome Database

InterMOD

modENCODE Wiki

modMine

National Center for Biotechnology Information (NCBI)

National Center for Integrative Biomedical Informatics (NCIBI)

N-Browse

Online Mendelian Inheritance in Man (OMIM)

PhenoBank Database

RNAi Database

Sanger Institute Databases

UCSC Genome Browser

S. cerevisiae Genome Database

S. pombe Genome Database

Programs and Tools[edit]

AddGene - Fire Vector Kit

Amplify 3 PCR program

Antibody validation

Antigenic peptides (Dana Farber)

BioNumbers

Fosmid Transgenes

Random Number Generator

Style Points and Conventions

miRNA resources[edit]

miRNAs: Sequence databases[edit]

Name Description Link
miRBase  Registry and categorization of of pre-miRNAs and mature miRNAs http://mirbase.org
Ensembl  miRNA gene and transcript sequences; splice variants; phylogenetic information; orthologs and paralogs  http://ensembl.org
GenBank (NCBI)  miRNA gene, transcript, mature sequences; annotations; links to other databases http://www.ncbi.nlm.nih.gov/genbank





miRNAs: Resources for miRNA target prediction
[edit]

Name Description Link
miRanda  Visualization of miRNA target sites mapped to target mRNAs; predictions for 5 species; search by miRNA or target; http://microrna.org
TargetScan Predictions for 10 species; search by  miRNA, target, or miRNA families; conservation filter; http://targetscan.org
DIANA-microT  Validated miRNA targets (TarBase); associations of miRNAs with KEGG pathways (mirPath); analysis of expression data for
miRNA function (DIANA-mirExTra); target prediction (DIANA-microT); search by miRNA, targets, or both;
http://diana.cslab.ece.ntua.gr/microT
PITA Target predictions for 4 species; filter predictions based on mismatches and conservation; search by miRNA or target;  http://genie.weizmann.ac.il/pubs/mir07
PicTar Search by miRNA or target;  http://pictar.mdc-berlin.de
TargetSpy Predictions for 5 species; sensitive vs. specific prediction filters;  http://targetspy.org
miRDB Expression-based target predictions from MirTarget2; predictions for 5 species; incorporates predictions from TargetScan, PicTar,
miRanda, and MirTarget;
http://mirdb.org
miRecords Database of experimentally validated miRNA targets; database of miRNA target predictions from 11 algorithms for 9 species; http://mirecords.biolead.org
miRWalk Database of predicted and validated miRNA:target interactions from 8 algorithms for 3 species; predicted targets mapped to
pathways and diseases; validated targets mapped to organs and cell lines;
http://mirwalk.uni-hd.de
starBase Database of sequencing experiments mapping miRNA binding sites to mRNAs; incorporates predictions from 6 algorithms for
6 species; search by miRNA or target; tools for functional enrichment analysis of miRNA targets (GO, KEGG)
http://starbase.sysu.edu.cn
TarBase
miRecords
miRTarBase
Integrated collection of analyses from experimental and predicted approaches http://microrna.gr/tarbase
http://mirecords.umn.edu/mirecords
http://mirtarbase.mbc.nctu.edu.tw
miRNA_Targets Predicted miRNA targets on full length mRNAs http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html
DIANA-LncBase Predicted and verified miRNA targets on long non-coding RNAs http://www.microrna.gr/LncBase



miRNAs: Functional and mapping databases[edit]

Name Description Link
miR2Disease Manually curated database of miRNa dysregulation in human diseases  http://mir2disease.org
miRGator 2.0 miRNA portal: miRNA diversity, expression profiles, target relationships, supporting tools  http://mirgator.kobic.re.kr
PhenomiR2.0 Database of information about differentially regulated miRNA expression in diseases and biological processes  http://mips.helmholtz-muenchen.de/phenomir
miRo database miR ontology database http://ferrolab.dmi.unict.it/miro





miRNAs: Expression and gene regulation[edit]

Name Description Link
mirZ Visualization and prediction of miRNA targets http://www.mirz.unibas.ch/
microRNA.org

Predicted miRNA targets and target downregulation scores

Experimentally observed expression patterns

http://microRNA.org
dbDEMC Database of differentially expressed miRNAs in human cancers  http://159.226.118.44/dbDEMC/index.html
miRStart Database of miRNA transcription start sites (human) http://mirstart.mbc.nctu.edu.tw
TransmiR Database for miRNA-TF regulations http://cmbi.bjmu.edu.cn/transmir
PuTmiR Database for extracting neighboring TFs of human miRNAs http://www.isical.ac.in/~bioinfo_miu/TF-miRNA/TF-miRNA.html
CircuitsDB Database of miRNA/TF regulatory circuits in human and mouse  http://biocluster.di.unito.it/circuits
MIR@NT@N miRNA and transcription factor analysis network http://mironton.uni.lu
miRandola Extracellular/circulating miRNA database  http://atlas.dmi.unict.it/mirandola





miRNAs: Web tools
[edit]

Name Description Link
MiRror
http://protos.cs.huji.ac.il/mirror
MMIA miRNA and mRNA integrated analysis http://cancer.informatics.indiana.edu/mmia
SylArray Web server for automated detection of miRNA effects from expression data  http://www.ebi.ac.uk/enright-srv/sylarray/
MiRonTop Mining miRNA targets across large scale gene expression studies http://microarray.fr:8080/miRonTop/index
TAM Tool for annotation of miRNAs http://cmbi.bjmu.edu.cn/tam
MAGIA miRNA and gene integrated analysis web tool http://gencomp.bio.unipd.it/magia
miRo miRNA ontology database http://ferrolab.dmi.unict.it/miro/
YM500 Integrative small RNA sequencing database: miR quantification, isomiR identification, and novel miR prediction http://ngs.ym.edu.tw/ym500/
RNA22-GUI Web-based application for interactive exploration and in-context visualization of miRNA target predictions using RNA22 

http://cm.jefferson.edu/rna22v1.0/

piRNA resources[edit]

piRNAs: Sequence databases[edit]

Name Description Link
piRNABank Web analysis system and resource providing information on piRNAs in multiple species.  http://pirnabank.ibab.ac.in/
piRNAcluster Database of piRNA clusters from select mammalian species.  http://www.uni-mainz.de/FB/Biologie/Anthropologie/492_ENG_HTML.php




ncRNA resources[edit]

ncRNAs: Comprehensive data resources[edit]

Name Description Link
NRDR Non-coding RNA Database Resource http://www.ime.usp.br/~durham/ncrnadatabases/index.php
deepBase Platform for annotating and discovering ncRNAs from NGS data.  http://deepbase.sysu.edu.cn/index.php
MODOMICS Database of RNA modification pathways http://modomics.genesilico.pl