OrthoClust – Orthology-based Network Framework for Clustering data across multiple Species

OrthoClust

:: DESCRIPTION

OrthoClust is a clustering algorithm built on a multilayer network framework. It concatenates networks from individual species by their orthology relationships, arriving at a multiplex network. By optimizing the a generalized modularity function, OrthoClust returns a set of modules that could be either conserved or species-specific.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

OrthoClust

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.
OrthoClust: an orthology-based network framework for clustering data across multiple species.
Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

PubNet – Publication Network Graph Utility

PubNet

:: DESCRIPTION

 PubNet is a utility that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005).
Genome Biol 6:R80.

NetAutoProbit – Network Auto-Probit Modeling for Binary Network Processes

NetAutoProbit

:: DESCRIPTION

NetAutoProbit is a matlab software of network-based auto-probit method for protein function prediction.

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 NetAutoProbit

:: MORE INFORMATION

Citation

Biometrics. 2011 Sep;67(3):958-66. doi: 10.1111/j.1541-0420.2010.01519.x. Epub 2010 Dec 6.
Network-based auto-probit modeling for protein function prediction.
Jiang X, Gold D, Kolaczyk ED.

CrossTalkZ 1.4 – Statistical tool to assess Crosstalk Enrichment between Node Groupings in a Network

CrossTalkZ 1.4

:: DESCRIPTION

CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

 CrossTalkZ

:: MORE INFORMATION

Citation

PLoS One. 2013;8(1):e54945. doi: 10.1371/journal.pone.0054945. Epub 2013 Jan 23.
Statistical assessment of crosstalk enrichment between gene groups in biological networks.
McCormack T, Frings O, Alexeyenko A, Sonnhammer EL.

MGclus – Network Clustering Employing shared Neighbors

MGclus

:: DESCRIPTION

MGclus is a new algorithm designed to detect modules with a strongly interconnected neighborhood in large scale biological interaction networks.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

 MGclus

:: MORE INFORMATION

Citation

Mol Biosyst. 2013 Jul;9(7):1670-5. doi: 10.1039/c3mb25473a. Epub 2013 Feb 11.
MGclus: network clustering employing shared neighbors.
Frings O, Alexeyenko A, Sonnhammer EL.

GeneNT 1.4.1 – Relevance or Dependency network and Signaling Pathway Discovery

GeneNT 1.4.1

:: DESCRIPTION

GeneNT is a R package to estimate co-expression gene networks

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/ Linux
  • R package

:: DOWNLOAD

 GeneNT

:: MORE INFORMATION

Citation:

Network constrained clustering for gene microarray data.
Zhu D, Hero AO, Cheng H, Khanna R, Swaroop A.
Bioinformatics. 2005 Nov 1;21(21):4014-20.

BIANA 1.4.5 – Biologic Interaction and Network Analysis

BIANA 1.4.5

:: DESCRIPTION

BIANA (Biologic Interactions and Network Analysis) is a biological database integration and network management framework written in Python. It uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BIANA

:: MORE INFORMATION

Citation

Biana: a software framework for compiling biological interactions and analyzing networks.
Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B.
BMC Bioinformatics. 2010 Jan 27;11:56.

canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

EnrichNet 1.1 – Network-based Enrichment Analysis

EnrichNet 1.1

:: DESCRIPTION

EnrichNet is a network-based enrichment analysis method to identify functional associations between user-defined gene or protein sets and cellular pathways. The datasets are mapped onto a protein interaction network (or other user-defined molecular network) and their pairwise associations are assessed by computing a graph-based statistic, i.e. distances between the network nodes are mapped against a background model. In contrast to the classical overlap-based enrichment analysis, associations can also be identified for non-overlapping gene/protein sets and the user can investigate them in detail by visualizing corresponding sub-graphs.

::DEVELOPER

EnrichNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.
EnrichNet: network-based gene set enrichment analysis.
Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.