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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)


The Worm Breeder's Gazette

Worm ORFeome




The WormImage Database 

Databases (Other)[edit]

The Coli Genetic Stock Center


Interactome Database


modENCODE Wiki


National Center for Biotechnology Information (NCBI)

National Center for Integrative Biomedical Informatics (NCIBI)


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)


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
Ensembl  miRNA gene and transcript sequences; splice variants; phylogenetic information; orthologs and paralogs
GenBank (NCBI)  miRNA gene, transcript, mature sequences; annotations; links to other databases

miRNAs: Resources for miRNA target prediction

Name Description Link
miRanda  Visualization of miRNA target sites mapped to target mRNAs; predictions for 5 species; search by miRNA or target;
TargetScan Predictions for 10 species; search by  miRNA, target, or miRNA families; conservation filter;
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;
PITA Target predictions for 4 species; filter predictions based on mismatches and conservation; search by miRNA or target;
PicTar Search by miRNA or target;
TargetSpy Predictions for 5 species; sensitive vs. specific prediction filters;
miRDB Expression-based target predictions from MirTarget2; predictions for 5 species; incorporates predictions from TargetScan, PicTar,
miRanda, and MirTarget;
miRecords Database of experimentally validated miRNA targets; database of miRNA target predictions from 11 algorithms for 9 species;
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;
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)
Integrated collection of analyses from experimental and predicted approaches
miRNA_Targets Predicted miRNA targets on full length mRNAs
DIANA-LncBase Predicted and verified miRNA targets on long non-coding RNAs

miRNAs: Functional and mapping databases[edit]

Name Description Link
miR2Disease Manually curated database of miRNa dysregulation in human diseases
miRGator 2.0 miRNA portal: miRNA diversity, expression profiles, target relationships, supporting tools
PhenomiR2.0 Database of information about differentially regulated miRNA expression in diseases and biological processes
miRo database miR ontology database

miRNAs: Expression and gene regulation[edit]

Name Description Link
mirZ Visualization and prediction of miRNA targets

Predicted miRNA targets and target downregulation scores

Experimentally observed expression patterns
dbDEMC Database of differentially expressed miRNAs in human cancers
miRStart Database of miRNA transcription start sites (human)
TransmiR Database for miRNA-TF regulations
PuTmiR Database for extracting neighboring TFs of human miRNAs
CircuitsDB Database of miRNA/TF regulatory circuits in human and mouse
MIR@NT@N miRNA and transcription factor analysis network
miRandola Extracellular/circulating miRNA database

miRNAs: Web tools

Name Description Link
MMIA miRNA and mRNA integrated analysis
SylArray Web server for automated detection of miRNA effects from expression data
MiRonTop Mining miRNA targets across large scale gene expression studies
TAM Tool for annotation of miRNAs
MAGIA miRNA and gene integrated analysis web tool
miRo miRNA ontology database
YM500 Integrative small RNA sequencing database: miR quantification, isomiR identification, and novel miR prediction
RNA22-GUI Web-based application for interactive exploration and in-context visualization of miRNA target predictions using RNA22

piRNA resources[edit]

piRNAs: Sequence databases[edit]

Name Description Link
piRNABank Web analysis system and resource providing information on piRNAs in multiple species.
piRNAcluster Database of piRNA clusters from select mammalian species.

ncRNA resources[edit]

ncRNAs: Comprehensive data resources[edit]

Name Description Link
NRDR Non-coding RNA Database Resource
deepBase Platform for annotating and discovering ncRNAs from NGS data.
MODOMICS Database of RNA modification pathways