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miRvestigator Framework

The miRvestigator framework is designed to take as input a list of co-expressed genes and will return the most likely miRNA regulating these genes. It does this by searching for an over-represented sequence motif in the 3' untranslated regions (UTRs) of the genes using Weeder and then comparing this to the miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).

Enter Co-Expressed Gene List  [+]

Include Viral miRNAs:
Yes  No
Gene Identifier:
Name the gene list:
Enter gene IDs for the co-expressed genes (Entrez gene, Ensembl gene, RefSeq transcript or official gene symbol):
(Acceptable delimiters include: comma, space, tab or newline)
Or load sample data: [+]
C. elegans
D. melanogaster
G. gallus
H. Sapiens
M. musculus
R. norvegicus
Kaposi-Sarcoma-Associated Herpes Virus
D. rerio
Parameters for Weeder  [+]
Motif Sizes:
Background Model:
Target Site Quality:
Parameters for miRvestigator HMM  [+]
Seed Models:
6mer 7mer 8mer
Model Wobble Base-Pairing:
Yes No
Min. Freq. of G or U:
Submit the Job
Top miRNAs to return:
Notify by email when finished: (Optional)

Need help? Please contact wwu(at)systemsbiology.org if you have any questions, comments or concerns.
Developed at the Institute for Systems Biology in the Baliga Lab.