:: DESCRIPTION
CORNA is a package for R that analyses microarray data and miRNA target prediction data to find statistically over-represented miRNA-target relationships.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Mar 15;25(6):832-3. doi: 10.1093/bioinformatics/btp059. Epub 2009 Jan 29.
CORNA: testing gene lists for regulation by microRNAs.
Wu X1, Watson M.
:: DESCRIPTION
TRES is a novel web tool that predicts the likely upstream regulators for a given gene list.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
TRES predicts transcription control in embryonic stem cells.
Pooley C, Ruau D, Lombard P, Gottgens B, Joshi A.
Bioinformatics. 2014 Jun 23. pii: btu399.
:: DESCRIPTION
DCGL is an R package for differential co-expression analysis (DCEA) and differential regulation analysis (DRA).
::DEVELOPER
System Biology Group, Shanghai Center for Bioinformation Technology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Nov 20;8(11):e79729. doi: 10.1371/journal.pone.0079729. eCollection 2013.
DCGL v2.0: an R package for unveiling differential regulation from differential co-expression.
Yang J1, Yu H, Liu BH, Zhao Z, Liu L, Ma LX, Li YX, Li YY.
:: DESCRIPTION
BIRTA uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.
::DEVELOPER
Benedikt Zacher <zacher at lmb.uni-muenchen.de>, Holger Froehlich <frohlich at bit.uni-bonn.de>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jul 1;28(13):1714-20. doi: 10.1093/bioinformatics/bts257. Epub 2012 May 4.
Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.
Zacher B1, Abnaof K, Gade S, Younesi E, Tresch A, Fr?hlich H.
:: DESCRIPTION
TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.
::DEVELOPER
the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.
:: DESCRIPTION
ARN(Autophagy Regulatory Network) is an integrated resource to analyze regulatory network of autophagy proteins
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Autophagy. 2015;11(1):155-65. doi: 10.4161/15548627.2014.994346.
Autophagy Regulatory Network – a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy.
Türei D1,et al.
:: DESCRIPTION
RACER fits the mRNA expression as response using as explanatory variables the TF binding signals (TFBS) from ENCODE, CNV, DM, miRNA expression signals from TCGA. Briefly, RACER infers the sample-specific TF/miRNA regulator activities, which are then used as inputs to infer specific TF/miRNA-gene interactions. The two-stage regression circumvents the problem with integrating the non-sample-specific ENCODE TFBS with the sample-specific TCGA measurements.
::DEVELOPER
Yue Li ,The Zhang Lab, University of Toronto
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Li Y, Liang M, Zhang Z (2014)
Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia.
PLoS Comput Biol 10(10): e1003908. doi:10.1371/journal.pcbi.1003908
:: DESCRIPTION
rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.