Tools and data sets for network analysis
(for network analysis contact Dr. Giovanni Scardoni, CBMC)
Data sets are compiled from public data-bases and from literature and manually curated for accuracy. They are intended for network reconstruction, topological and multidimensional analysis in cell biology (see a biological network analysis paper).
Data-sets are in Cytoscape-ready formats [.sif (network), .cys (network+attributes), .NA (node attribute), .EA (edge attribute), .txt or .xls (list of molecules or tables of multiple attributes)].
Taxid is 9606 Homo sapiens.
Gene/protein ID is provided by HGNC. Different IDs are converted to HGNC IDs and cross-checked with: g:profiler, biodb, cronos, geneIDconverter, picr, and bridgeDB.
Interactomic (PPI) data sets are compiled from: Pathway commons_hs, MiMI, BCI, DIP, BioGRID, HPRD, IntAct, MINT, PiNA, HiNT, UniHI, ConsensusPathDB, SignaLink 2.0, HIPPIE, HAPPI, MENTHA, SIGNOR and from literature.
For signaling_networks see here and this link.
For phospho_network data see: dbPTM, PhosphoSite, PhosphoPoint, PhosphoELM, Kinome, UNIPROT kinase, PHOSIDA, PhosphoNet, KEA.
For protein_domains see: PDB, PawsonLab, Cell Signaling domains, CATH, CDD, SMART, Pfam, 3DID, InterPro, STRING, PPEP, DOMINO.
For gene onthologies see: GO database.
For enriched network analysis see: GeneCards, Enrichr, BioGPS, Panther, ProteinQuest (upon license).
For disease_networks see: MalaCards, DISEASE, DisGeneNet, OMIM, GAD, Diseasome
Go here for CBMC-developed network topological analysis tools; here for the Cytoscape plugins usage-chart.
Go to CentiServer for a comprehensive web-based resource for computation of network centrality indexes.
Downloadable files:
(for network analysis contact Dr. Giovanni Scardoni, CBMC)
Data sets are compiled from public data-bases and from literature and manually curated for accuracy. They are intended for network reconstruction, topological and multidimensional analysis in cell biology (see a biological network analysis paper).
Data-sets are in Cytoscape-ready formats [.sif (network), .cys (network+attributes), .NA (node attribute), .EA (edge attribute), .txt or .xls (list of molecules or tables of multiple attributes)].
Taxid is 9606 Homo sapiens.
Gene/protein ID is provided by HGNC. Different IDs are converted to HGNC IDs and cross-checked with: g:profiler, biodb, cronos, geneIDconverter, picr, and bridgeDB.
Interactomic (PPI) data sets are compiled from: Pathway commons_hs, MiMI, BCI, DIP, BioGRID, HPRD, IntAct, MINT, PiNA, HiNT, UniHI, ConsensusPathDB, SignaLink 2.0, HIPPIE, HAPPI, MENTHA, SIGNOR and from literature.
For signaling_networks see here and this link.
For phospho_network data see: dbPTM, PhosphoSite, PhosphoPoint, PhosphoELM, Kinome, UNIPROT kinase, PHOSIDA, PhosphoNet, KEA.
For protein_domains see: PDB, PawsonLab, Cell Signaling domains, CATH, CDD, SMART, Pfam, 3DID, InterPro, STRING, PPEP, DOMINO.
For gene onthologies see: GO database.
For enriched network analysis see: GeneCards, Enrichr, BioGPS, Panther, ProteinQuest (upon license).
For disease_networks see: MalaCards, DISEASE, DisGeneNet, OMIM, GAD, Diseasome
Go here for CBMC-developed network topological analysis tools; here for the Cytoscape plugins usage-chart.
Go to CentiServer for a comprehensive web-based resource for computation of network centrality indexes.
Downloadable files:
Homo sapiens, non-redundant, undirected, no-loops, physical protein-protein binary interaction data set in Cytoscape .sif format
(16057 unique protein HGNC IDs - 364816 binary interactions; compiled from Pathway commons_hs + MiMI + BCI + DIP + BioGRID + HPRD + HiNT + UniHI + ConsensusPathDB) and from literature
Homo sapiens, non-redundant, undirected, no-loops, physical protein-protein binary interaction data set in Cytoscape .cys format (13890 unique protein HGNC IDs - 127697 binary interactions; compiled from BioGRID)
Homo sapiens, protein-protein, DIRECTED, no-loops, functional and physical interaction data set, extracted from Pathway Commons and converted to HGNC IDs, in Cytoscape .sif format (1289432 interactions)
List of edge attributes for the PathwayCommons.sif data set (see below PathwayCommons_Interaction_rules). It allows generating directed networks showing the informational flow in the network
Binary interaction rules describing the meaning of edge attributes in PathwayCommons_SignalingFlow.EA data set (from http://www.pathwaycommons.org/pc/sif_interaction_rules.do)
Directed PPI signaling network with edge attributes of type state_change (about 77560 interactions)
List of edge attributes to generate directed PPI signaling networks with edge attributes of type state_change (about 77560 interactions)
Directed PPI signaling network with edge attributes with information of type activation-inhibition-docking activity (about 63439 interactions)
List of edge attributes to generate directed PPI signaling networks with information of type activation-inhibition-docking activity (about 63439 interactions)
Homo sapiens, non-redundant, undirected, physical protein-protein binary interaction data set (14740 unique protein HGNC IDs - 253638 binary interactions) with information about protein domains/motifs involved in protein interactions; name of 471 domains/motifs are nodes in the network linked to corresponding proteins; node attributes are domain/motif type and specific name (27); edge attributes are domain/motifs name (471) and aa position for every domain/motif. Cytoscape.cys format (compiled from Pathway commons_hs + HPRD)
Network of pathway names_to_genes; interaction means that a gene belongs to the pathway; 3813 pathways; Cytoscape .sif format
Homo sapiens, non-redundant, undirected, physical protein-protein binary interaction data set (14740 unique protein HGNC IDs - 253638 binary interactions) with information about protein involved in diseases; diseases names are nodes in the network linked to involved proteins; Cytoscape.sif format; (compiled from Pathway commons_hs + OMIM + DisGeneNet + Diseasome)
Network of GENES to DISEASES (from "Network analysis of genes and their association with diseases" - Gene. 2016 Jun 2. pii: S0378-1119(16)30439-5; http://www.sciencedirect.com/science/article/pii/S0378111916304395)
List of signaling pathways (3811)
Complete list of homo sapiens kinases
Complete list of homo sapiens phosphatases
Complete list of homo sapiens kinase domains
Table of protein domains (ID = HGNC)
Table of protein tissue and organ exprerssion (ID = HGNC)
Human proteins AA sequence
Table of protein post-translational modifications with modifying enzymes (from http://www.hprd.org/)
List of proteins found in focal adhesions (http://www.adhesome.org/index.htm)
List of gene_to_disesase (http://diseasome.eu/)
List of genes mapped to signaing pathways
List of genes involved in immune response (http://bioinf.uta.fi/Immunome/)
List of genes involved in Essential Hypertension (http://www.biomedcentral.com/1752-0509/7/32/abstract)
List of signaling proteins involved in inside-out integrin activation (= 66) (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360201/)
PPI network of first neighbors (FN) of signaling protein involved in integrin activation (= 66); (node = 3091; edge = 97115)
List of genes involved in coronary arthery disease
Gene Onthology annotations mapped on HGNC IDs (CELLULAR_COMPONENT - MOLECULAR_FUNCTION - BIOLOGICAL_PROCESS) compiled from GO database
Table of human protein IDs from HGNC with cross annotations
List of proteins interacting with PIP2 (1,4,5 and 1,3,4,5) (from Catimel B, Schieber C, Condron M, Patsiouras H, Connolly L, Catimel J, Nice
EC, Burgess AW, Holmes AB. The PI(3,5)P2 and PI(4,5)P2 interactomes. J Proteome Res. 2008 Dec;7(12):5295-313. PubMed PMID: 19367725.)
Table of genes for which mutations have been causally implicated in cancer (http://cancer.sanger.ac.uk/cancergenome/projects/census/)
Table of genes causally implicated in cancer (http://ncg.kcl.ac.uk/index.php)
Table of cancer driver genes. From "Cancer Genome Landscapes" (http://www.sciencemag.org/content/339/6127/1546.full)
List of signaling proteins and miRs involved in the pathogenesis of B-CLL (see also B-CLL page)
List of genes (24) associated to Alzheimer's disease (see http://www.nature.com/ng/journal/v45/n12/full/ng.2802.html and http://www.nature.com/nature/journal/v505/n7484/full/nature12825.html for PLD3 data)
List of proteins with the corresponding PDB ID entry (crystallography) (From http://idconverter.bioinfo.cnio.es)
List of human protein IDs from HGNC