Data-sets for biological network analysis - Cytoscape format
(periodically controlled and/or updated for accuracy and completeness - Last update: 16/04/2019)
WARNING: UBC and UBB genes are stress-regulated polyubiquitin genes in mammals. They plays a key role in maintaining cellular ubiquitin levels under stress conditions. In the HUMAN-INTERACTOME data-set (see below), UBC has 9647 first neighbours (direct interactors), accounting for 56% of total proteins, in turn connected by 301738 edges, accounting for about 70% of total binary interactions. In contrast, UBB has 342 first neighbours (interactors), accounting for 2% of total proteins, in turn connected by 6679 edges, accounting for 1,8% of total binary interactions. Thus, together, UBB and UBC interact with 59% of total proteins, accounting for 70% of total binary interactions. This makes UBC the most connected protein in the HUMAN-INTERACTOME data-set, making very likely that UBC is systematically present in any sub-network eventually generated, showing the highest degree. UBC presence does reflect the central role of polyubiquitin in protein expression and turn-over regulation, but not necessarily must be considered when singling mechanisms have to be analysed. Indeed, UBC presence in networks will alter topological analysis since UBC displays a dominant topological role (degree). Thus, we suggest removing UBC, and eventually UBB, from generated sub-networks every time topological analysis, such as centrality indexes calculation, has to be performed in the context of signalling networks. This will provide the real topological role of a specific signalling protein, and thus its functional relevance, in absence of ubiquitination.
(periodically controlled and/or updated for accuracy and completeness - Last update: 16/04/2019)
WARNING: UBC and UBB genes are stress-regulated polyubiquitin genes in mammals. They plays a key role in maintaining cellular ubiquitin levels under stress conditions. In the HUMAN-INTERACTOME data-set (see below), UBC has 9647 first neighbours (direct interactors), accounting for 56% of total proteins, in turn connected by 301738 edges, accounting for about 70% of total binary interactions. In contrast, UBB has 342 first neighbours (interactors), accounting for 2% of total proteins, in turn connected by 6679 edges, accounting for 1,8% of total binary interactions. Thus, together, UBB and UBC interact with 59% of total proteins, accounting for 70% of total binary interactions. This makes UBC the most connected protein in the HUMAN-INTERACTOME data-set, making very likely that UBC is systematically present in any sub-network eventually generated, showing the highest degree. UBC presence does reflect the central role of polyubiquitin in protein expression and turn-over regulation, but not necessarily must be considered when singling mechanisms have to be analysed. Indeed, UBC presence in networks will alter topological analysis since UBC displays a dominant topological role (degree). Thus, we suggest removing UBC, and eventually UBB, from generated sub-networks every time topological analysis, such as centrality indexes calculation, has to be performed in the context of signalling networks. This will provide the real topological role of a specific signalling protein, and thus its functional relevance, in absence of ubiquitination.
Homo sapiens, undirected, non-redundant, no-loops, physical protein-protein binary interaction data set in Cytoscape .sif format (18333 unique protein HGNC IDs - 586972 binary interactions - updated on 23/03/2021). Compiled from InBio Map + Pathway commons_hs + IntAct + MiMI + BCI + DIP + BioGRID + HPRD + HiNT + UniHI + ConsensusPathDB + Signor 2.0 + SignaLink 2.0 + HAPPI + HIPPIE + CCSB) and from manually-curated literature survey. The data-set includes only experimentally multi-verified PP binary interactions. Predicted interactions and not cross-verified, binary interactions are excluded. [See OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nat Methods. 2016 Nov 29;13(12):966-967. PMID: 27898060 DOI: 10.1038/nmeth.4077]
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 (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; 6013 pathways; Cytoscape .sif format
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)
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; from "The expanded human disease network combining protein–protein interaction information" - http://www.nature.com/ejhg/journal/v19/n7/full/ejhg201130a.html)
Homo sapiens, undirected, non-redundant, no-loops, physical protein-protein binary interaction data set in Cytoscape .sif format (16802 unique protein HGNC IDs - 326341 binary interactions - updated on 04/04/2017) integrated with Expanded_GENE_to_DISEASE_Network. Compiled from InBio Map + Pathway commons_hs + IntAct + MiMI + BCI + DIP + BioGRID + HPRD + HiNT + UniHI + ConsensusPathDB + Signor 2.0 + SignaLink 2.0 + HAPPI + HIPPIE + CCSB) and from manually-curated literature survey. The data-set includes only experimentally verified PP binary interactions. Predicted interactions and high-throughput, two-hybrid, not individually verified, interactions are excluded. [See OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nat Methods. 2016 Nov 29;13(12):966-967. PMID: 27898060 DOI: 10.1038/nmeth.4077]
PPI network of first neighbors (FN) of signaling protein involved in integrin activation modulation (= 71); (nodes = 3687; edges = 103322)
List of proteins involved in apoptosis regulation
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/)
Expanded list of gene_to_disesase (from "The expanded human disease network combining protein–protein interaction information" - http://www.nature.com/ejhg/journal/v19/n7/full/ejhg201130a.html)
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 integrin activation modulation (either positive or negative modulation; total = 72 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360201/)
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 (20/02/2017)
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)
Expanded list of proteins with the corresponding PDB ID entry (crystallography) (From http://www.uniprot.org/)
List of human protein IDs from HGNC (20/02/2017)
List of genes regulated by corresponding miRNAs