Resources for Biological Network Analysis |
[Adopted from Insuk Lee's page from UT Austin] |
Tools 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 Cytoscape 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 RegulonDB BioCyc 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 RNAi DB National Bioresource Project (C. elegans deletion mutants) C. elegans gene knockout consortium Mark Vidal's worm interactome Fly Links FlyBase Y2H_by_Curagen Mycobacteria Links NIH TB research section Malaria Links Winzeler lab PlasmoDB Arabidopsis and other model plant Links TAIR Plant ontology consortium SeedGenes Project (essential genes in Arabidopsis) Populus Genome Consortium Brachypodium.org :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) GeneCards 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 PeptideProphet ProteinProphet 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) IPAM KITP online lecture: bio-molecule network |