Resources for Biological Network Analysis

[Adopted from Insuk Lee's page from UT Austin]


SNAP: Stanford Network Analysis Package (C++ netork analysis library).
Boost Graph Library:official_site Manunal
Gnuplot (2D, 3D plot open software):home Tutorial_1 Tutorial_2
SBML: Systems Biology Markup Language.
Grace (2D plot open software)
LGL (Large Graph Layout) by University of Texas, Austin
NetworkX a Python library for network analysis.
VisANT (An integrative Visual Analysis Tool for Biological Networks and Pathways
Cortona VRML client (Interactive Web3D viewer)
BioLayout Java
igraph graph manipulation tool library (works with R)
Pajek (Drawing and analysis of network on Windows platform)
MCL (Markov cluster algorithm)
Xcluster (by Stanford)
Graemlin (network comparison tool)
Network comparison toolkits
FANMOD (network motif detection)

Species Interaction Data
Interaction Web Database.
Barabasi Group Network Data (metabolic + PPI)

Genome Annotation
MIPS (Munich Information center for Protein Sequences)
KEGG (Kyoto Encyclopedia of Genes and Genomes)
GO (Gene Ontology)
Ensembl: Genome browser (for many Eukaryotic genomes)
Reactome: A knowledgebase of biological process
Bioverse: Proteome annotation

Orthology Identification
InParanoid: Eukaryotic orthology groups
P-POD: Princeton Protein Orthology Database
COGs: Clusters of Orthologous Groups
EGO: Eukaryotic Gene Orthologues
OrthoMCL DB: Ortholog Groups of Protein Sequences

Kinome and Cancer Data
The Human Kinome.
Other kinomes.
NetworKIN: Phosphorylation Networks.
Cancer Cell Map

Protein Interaction
IMEx: the International Molecular Exchange consortium
DIP: Database of Interacting Proteins by UCLA
IntAct: Database of Interacting Proteins by EBI
GRID: General Repository for Interaction Datasets
MINT: Molecular INTeraction Datasets
UniHI: Unified Human Interactome
Yeast TAP Project
TRANSFAC: Transcription Factor Database by Dr. Wingender (Germany)
STRING : by P. Bork
Predictome: similar to STRING
InterPreTS: Interaction Prediction through Tertiary Structure
Prolinks: by UCLA Eisen group

Yeast Links
SGD: yeast Saccharomyces cerevisiae database
Yeast gfp localization by UCSF
TRIPLE (a database of TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces)
SGDP Saccharomyces Genome Deletion Project)
Yeast orfome: yeast gene definition update by Yale
Saccharomyces Cerevisiae Morphological Database: yeast quantitative trait DB

Worm Links
worm server
Worm Base
Worm Book
C. elegans Resources
EDGE (c.Elegans Differential Gene Expression) db
National Bioresource Project (C. elegans deletion mutants)
C. elegans gene knockout consortium
Mark Vidal's worm interactome

Fly Links

Mycobacteria Links
NIH TB research section

Malaria Links
Winzeler lab

Arabidopsis and other model plant Links
Plant ontology consortium
SeedGenes Project (essential genes in Arabidopsis)
Populus Genome Consortium :a New model plant
Carnegie Institute Dept of Plant Biology
Danforth Plant Science Center
QTL references
Virtual Plant

Rice and other crop Links
TIGR Rice Genome Annotation
Rice Annotation Project (RAP-DB)
Gramene: A Resource for Comparative Grass Genomics
Solanaceae Genomics Network
Ronald Lab (UC Davis Rice group)
Yale Rice Project

Mouse Links
The Jackson Laboratory
Mouse Genome Informatics MIG ftp
Mouse Phenome Database by Jackson Laboratory
MRC Mammalian Genetics Unit/Harwell
International Mammalian Genome Society

Human Links
Gene Network
The Human Genome (Introduction to the human genome by Sanger)
ID-serve: by UT
Human Protein Reference DB
Human Genome Nomenclature committee (HGNC)
Comprehensive human transcriptome by Rosetta Impharmatics

Microarray Links
Gene Network Central
ArrayExpress (by EBI)
GEO (Gene Expression Omnibus by NCBI)
AfCS (Alliance for Cellular Signaling )
SMD (Stanford Microarray DB)
NASCArrays (most data for Arabidopsis)

Weigel World (Affy microarray data for Arabidopsis)

Collateral Missing Value Estimation (CMVE) Software(Good imputation tool)

Mass spectrometry-based proteomics
Yates Lab : SEQUEST algorithm resource
Scripps center for mass spectropy
MatrixScience : Mascot agorithm resource
ProteinProspector : for mining sequence DB in conjunction with MS experiments by UCSF
Matthias Mann Group
Aebersold Group
ProbID : spectra matching program by ISB
Delta Mass: Post Translational Modification Mass shift DB

Other Links
GTL (DOE Genomics Genome To Life)
HapMap (Haploid mapping project)
Network DB (by Newman)
DISOPRED2 (Intrinsic disorderness prediction)
BRITE (Biomolecular Relations in Information Transmission and Expression)
KITP online lecture: bio-molecule network