Cancerin – Infer Competing Endogenous RNA (ceRNA) interactions in Cancer

Cancerin

:: DESCRIPTION

Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Cancerin

:: MORE INFORMATION

Citation

Do D, Bozdag S.
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
PLoS Comput Biol. 2018 Jul 16;14(7):e1006318. doi: 10.1371/journal.pcbi.1006318. PMID: 30011266; PMCID: PMC6072113.

PathwaysWeb 2.0 – Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning

PathwaysWeb 2.0

:: DESCRIPTION

PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.

::DEVELOPER

PathwaysWeb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.

GenomicInteractions 1.26.0 – Exploring Chromatin interaction data

GenomicInteractions 1.26.0

:: DESCRIPTION

GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows  / MacOsX
  • R/Bioconductor

:: DOWNLOAD

GenomicInteractions

:: MORE INFORMATION

Citation:

Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B.
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.
BMC Genomics. 2015 Nov 17;16:963. doi: 10.1186/s12864-015-2140-x. PMID: 26576536; PMCID: PMC4650858.

PLIC – Protein-ligand Interaction Clusters

PLIC

:: DESCRIPTION

PLIC is a database of protein-ligand interaction clusters.

::DEVELOPER

Chandra lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Anand P, Nagarajan D, Mukherjee S, Chandra N.
PLIC: protein-ligand interaction clusters.
Database (Oxford). 2014 Apr 23;2014(0):bau029. doi: 10.1093/database/bau029. PMID: 24763918; PMCID: PMC3998096.

MTide – Identification of miRNA-target Interaction in Plants

MTide

:: DESCRIPTION

MTide is an integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MTide

:: MORE INFORMATION

Citation

MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Zhang Z, Jiang L, Wang J, Chen M.
Bioinformatics. 2014 Sep 24. pii: btu633.

ScanSite 4.0 – Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover

ScanSite 4.0

:: DESCRIPTION

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

::DEVELOPER

ScanSite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
Obenauer JC, Cantley LC, Yaffe MB.
Nucleic Acids Res. 2003 Jul 1;31(13):3635-41.

Hi-Jack – Pathway-based Inference of Host-pathogen Interactions

Hi-Jack

:: DESCRIPTION

Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

Hi-Jack

:: MORE INFORMATION

Citation:

Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions.
Kleftogiannis D, Wong L, Archer JA, Kalnis P.
Bioinformatics. 2015 Mar 9. pii: btv138

Genes2Networks 1.5 – Connecting Lists of Gene Symbols using Mammalian Protein Interactions databases

Genes2Networks 1.5

:: DESCRIPTION

Genes2Networks (G2N) is a tool that can be used to place lists of mammalian genes in the context of a background mammalian signalome and interactome networks. The input to the program is a list of human Entrez Gene gene symbols and background networks in SIG format, while the output includes: (a) all identified interactions for the genes/proteins, (b) a subnetwork connecting the genes/proteins using intermediate components that are used to connect the genes, (c) ranking of the specificity of intermediate components to interact with the list of genes/proteins.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Genes2Networks

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 4;8:372.
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
Berger SI, Posner JM, Ma’ayan A.

iPPI-Esml – Identifying Interactions of Proteins

iPPI-Esml

:: DESCRIPTION

iPPI-Esml is an ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iPPI-Esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.
Jia J, Liu Z, Xiao X, Liu B, Chou KC.
J Theor Biol. 2015 Apr 20. pii: S0022-5193(15)00173-3. doi: 10.1016/j.jtbi.2015.04.011.