About MANTRA 2.0
According to the Hindu tradition a Mantra is a sound, syllable, word or group of words capable of creating "spiritual transformation".
Mode of Action by NeTwoRk Analysis (MANTRA) is a computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”.
Getting Started
To understand the functioning of the different workspaces, you can explore the Interactive Workflow or download the official Tutorial Guide.
Input Format
The reference gene expression data-set used by MANTRA is part of the Connectivity Map (cmap) project based at the Broad Institute of MIT and Harvard (USA).
MANTRA supports two main input formats for analyzing novel drugs:
1) Microarray Analysis: Analyze raw data from Affymetrix experiments. The experiment
folder should contain Affymetrix .cel files only.
Supported Chips: HG-U133A, HT_HG-U133A, HG-U133A_2, HG-U133_Plus_2
Coming soon: HuEx-1_0-st, Human Agilent 4x44k
2) Ranked Gene Lists: Upload .txt files containing the 22,283 HG-U133A
probe-set identifiers sorted according to their differential expression following treatment.
Download Sample Data:
If these files are uploaded as input to MANTRA, the classification result obtained is described in Iorio et al. PNAS 2010.
Publications
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Carrella D, Napolitano F, Rispoli R, Miglietta M, Carissimo A, Cutillo L, Sirci F, Gregoretti F, di
Bernardo D.
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis.
Bioinformatics (2014) 30 (12): 1787-1788.
Abstract | PDF -
Iorio F, Isacchi A, di Bernardo D, Brunetti-Pierri N.
Identification of small molecules enhancing autophagic function from drug network analysis.
Autophagy, 2010 Nov 15;6(8):1204-5.
Abstract -
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R,
Brunetti-Pierri N, Isacchi A, di Bernardo D.
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Proc Natl Acad Sci U S A, 2010 August 17; 107: 14621-14626.
Abstract | PDF -
Iorio F, Tagliaferri R, di Bernardo D.
Identifying Network of Drug Mode of Action by Gene Expression Profiling.
Journal of Computational Biology, 2009; Feb;16(2):241-51.
Abstract | PDF -
Building Maps of Drugs Mode-of-Action from Gene Expression Data.
CIBB 2008, Revised Selected Papers 2009. Lecture Notes in Computer Science.
Abstract
PNAS paper Online Supporting Information (SI)
- SI Online - Figures and Tables
- SI Online - Impact of Rank Merging on the Performances
- SI Online - Communities and Rich-Clubs
- SI Online - Fuzzy GO Enrichments
- SI Online - Neighborhoods of the Tested Compounds
- SI Online - Signatures used to query the cMap in the Classic Way
- SI Online - Classic cMap Results
Contributors
MANTRA is maintained by di Bernardo Lab
members at TeleThon Institute of Genetics and Medicine (TIGEM).
Developed by Francesco Iorio and Diego di Bernardo.
Platform Migration & Modernization: Giacomo
Ferrillo.
License Agreement
Use of MANTRA tool is free to academic, government and non-profit users for non-commercial use. Commercial use requires a separate license agreement.
User Data Privacy: User data are stored permanently in our database and made freely available to everyone in the form of new "nodes" in the drug network (the raw transcriptional profiles are never made publicly available).