Biology Reference
In-Depth Information
TABLE 18.1
Tools and Repositories for Analysis and Visualization of Biological Networks
Tool
Application
Details
Bind
[210]
Repository of biomolecular interactions, 1500
þ
species
Static database (not updated)
BioGRID
[144]
Repository of genetic and protein interactions, model organisms (~50)
Database
DryGin
[211]
Repository of genetic interactions, yeast
Database
DIP
[212]
Repository of protein
protein interactions from 436 organisms
Database
e
ConsensusPathDB
[213]
Repository of biomolecular interactions, analysis of networks, 3 species Database
WEbInterViewer
[155]
Visualization and comparison of molecular networks
Web server
Torque
[214]
Small-scale, blast-based multi-species PPI search tool
Web server
GraphWeb
[215]
Retrival/analysis/visualization of molecular networks
Web server
String
[216]
Retrival/analysis/visualization of molecular networks, 1100
organisms Database
þ
Cytoscape
[217]
Biological network analysis and visualization
Software
Cytoscape/CyClus3D
[218]
Network clustering plug-on for Cytoscape
Plug-on
PathBlast
[219]
Blast-based multispecies PPI comparison/alignment tool
Web server
NetworkBlast
[220]
PPI analysis of protein complex identification
Web server
Neat
[221]
Analysis of networks and clusters
Web server
BioMet
[187]
Stoichiometric analysis and data integration tool for metabolic networks
Software/web server
Osprey
[222]
Visualization of biological networks
Software (last update: 2004)
VisAnt
[223]
Biological network analysis and visualization
Software/web server
Biological Networks
[224]
Analysis and visualization of heterogeneous biological data
Software
Babelomics
[225]
Integration and analysis of omics data
Web server
COBRA
[185]
MATLAB toolbox for simulation and analysis of metabolic networks
MATLAB Toolbox
SMBL toolbox
[186]
MATLAB toolbox for generating and modifying models in SMBL format MATLAB Toolbox
RefRec
[170]
Reconstruction and analysis of yeast biomolecular interaction network
Model distributed in SMBL format
Ondex
[226]
Graph-based analysis of high throughput data
Software
PPISearch
[227]
Blast-based multi-species analysis of pairs of interacting proteins
Web server
PathGuide
[228]
A list 325 pathway-related resources
Web page
DEEP
[229]
Integration of expression data with biological networks
Web server
GEOMI
[208,209]
Four-dimensional (4D) visualisation and analysis of protein interaction
networks.
Web server
knowledge of the characteristics and limitations of the
techniques used. As an example, high-throughput micro-
arrays and RNA sequencing (RNA-Seq) methods provide
complete information on changes in transcriptional
expression of all genes in an annotated genome (micro-
arrays)
[230]
or in the whole genome (coding and non-
coding regions; RNA-Seq)
[231]
, whereas proteome
quantitative methods often result in a much lower coverage
(
[232,233]
) and frequently contain missing values. A
careful integration of high-throughput 'omics' data will
need to address not merely normalization methods and/or
missing values, but the intrinsic limitations of the latest
techniques, with the latest bioinformatics and statistical
methods available. As a case example, high-throughput
transcriptome, proteome and metabolome data were
initially obtained from steady-state chemostat cultures in
a yeast systems biology study of cell growth under different
nutrient
limitations
[53]
. Since the 'omic' data were
