• Cytoscape

  • Referenced in 69 articles [sw09080]
  • surveyed, including a search for interaction pathways correlating with changes in gene expression, a study...
  • MetaCyc

  • Referenced in 28 articles [sw08243]
  • database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2097 pathways from more ... from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism ... representative sample of each experimentally elucidated pathway. MetaCyc is used in a variety of scientific ... data set for computationally predicting the metabolic pathways of organisms from their sequenced genomes, supporting...
  • GSA

  • Referenced in 37 articles [sw18747]
  • externally defined, for example, sets of gene pathways derived from biological databases. Our starting point...
  • Reactome

  • Referenced in 24 articles [sw14952]
  • free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive ... visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • simulations qualitatively reproduce the wild-type developmental pathway, as well as the outcome of various...
  • Plant-mPLoc

  • Referenced in 27 articles [sw22435]
  • proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide...
  • STRING

  • Referenced in 26 articles [sw23938]
  • from raw data repositories to highly formalized pathway databases. For many applications, a global view...
  • QPath

  • Referenced in 11 articles [sw35403]
  • QPath: a method for querying pathways in a protein-protein interaction network. Results: We present ... comprehensive framework for protein network searches using pathway queries. Given a linear query pathway ... QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins ... identified pathways. Matched pathways are automatically scored according to their variation from the query pathway...
  • E-CELL

  • Referenced in 22 articles [sw07917]
  • genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative...
  • Pathway Commons

  • Referenced in 9 articles [sw23072]
  • Pathway Commons, a web resource for biological pathway data. Pathway Commons ( http://www.pathwaycommons.org ... collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based ... browse and search a comprehensive collection of pathways from multiple sources represented in a common ... site that provides integrated bulk sets of pathway information in standard or convenient formats...
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Motivation: KEGG PATHWAY ... Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological ... software package to parse and analyze KEGG pathways with graph theory. Results: We introduce ... Bioconductor, an interface between KEGG pathways and graph models as well as a collection...
  • QNet

  • Referenced in 10 articles [sw13845]
  • used to study the evolution of molecular pathways across species. Querying such pathways ... paper, we significantly extend the class of pathways that can be efficiently queried...
  • Onto-Tools

  • Referenced in 10 articles [sw10974]
  • condition studied upon various biological processes and pathways. OE constructs functional profiles (using Gene Ontology ... genes present on the array represent specific pathways. Onto-Compare is a tool that allows...
  • HMDB

  • Referenced in 8 articles [sw28995]
  • GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive ... common toxins and environmental pollutants, SMPDB contains pathway diagrams for  25,000 human metabolic ... disease pathways, while FooDB contains equivalent information on  28,000 food components and food additives...
  • GenMAPP

  • Referenced in 7 articles [sw12317]
  • other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP ... data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms ... main features underlying GenMAPP are: Draw pathways with easy to use graphics tools. Color genes...
  • MRtrix

  • Referenced in 8 articles [sw19840]
  • unique potential to delineate the white matter pathways of the brain. However, methodologies currently available ... voxel, causing incorrect fiber orientations, and hence pathways, to be estimated through these voxels. Given...
  • SCAMP

  • Referenced in 11 articles [sw02112]
  • facilities, including: the ability to describe metabolic pathways of any structure and possessing any kinetics...
  • TRANSPATH

  • Referenced in 7 articles [sw08272]
  • database of mammalian signal transduction and metabolic pathways. As one of the earliest pathway databases...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression ... community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer...
  • PathBLAST

  • Referenced in 7 articles [sw29737]
  • interaction networks across species to identify protein pathways and complexes that have been conserved ... allows for functional annotation of protein interaction pathways based on similarity to the network...