ARN – Studying the Mechanism and Regulation of Autophagy

ARN

:: DESCRIPTION

ARN(Autophagy Regulatory Network) is an integrated resource to analyze regulatory network of autophagy proteins

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: 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.

RACER – Regression Analysis of Combinatorial Expression Regulation

RACER

:: 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

  • Windows / Linux
  • R

:: DOWNLOAD

 RACER

:: 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

rMAPS 2.0.0 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS 2.0.0

:: 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

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: 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.

TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: 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

  • Linux / Windows / MacOsX
  • Matlab
:: DOWNLOAD

 TIGER

:: 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.

BIRTA 1.14.0 – Bayesian Inference of Regulation of Transcriptional Activity

BIRTA 1.14.0

:: 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

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 BIRTA

:: 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.

PTRcombiner 1.1 – Mining combinatorial Regulation of Gene Expression from Post-transcriptional Interaction maps

PTRcombiner 1.1

:: DESCRIPTION

PTRcombiner is a tool for the study of the combinatorial nature of post-transcriptional trans-factors. It allows the identification of clusters of trans-factors (RBPs and miRNAs) from interaction maps and it performs the biological characterization of identified clusters giving information about the overlap among the target genes, the GO enrichments and similarity among GO terms.

::DEVELOPER

Andrea Passerini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 PTRcombiner

:: MORE INFORMATION

Citation

PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps.
Corrado G, Tebaldi T, Bertamini G, Costa F, Quattrone A, Viero G, Passerini A.
BMC Genomics. 2014 Apr 23;15:304. doi: 10.1186/1471-2164-15-304.

DCGL 2.0.2 – R package for unveiling differential Regulation from Differential Co-expression

DCGL 2.0.2

:: 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

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 DCGL

:: 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.

TRES – Transcription Regulation in Embryonic Stem Cell

TRES

:: DESCRIPTION

TRES is a novel web tool that predicts the likely upstream regulators for a given gene list.

::DEVELOPER

The Roslin Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: 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.

CORNA 1.3 – Testing Gene Lists for Regulation by microRNAs

CORNA 1.3

:: 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

CORNA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 CORNA

:: 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.