Data-sets, tools and procedures for network analysis
(for network analysis contact Prof.Carlo Laudanna or Dr. Giovanni Scardoni, CBMC)

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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, computational biology and systems 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:
InBio Map, OmniPath, Pathway commons_hs, MiMI, BCI, DIP, BioGRID, HPRD, IntAct, MINT, PiNA, HiNT, HuRI, PathPPI, UniHI, ConsensusPathDB, PSICQUIC, SignaLink 2.0, STRING, STITCH, HIPPIE, HAPPI, MENTHA, SIGNOR-2, and from literature.

Our compiled Human-Interactome.sif PPI interatomic data-set, was evaluated and cited in:
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.

For signalling networks see here.

For phospho-network data go to:
dbPTM, PhosphoSite, PhosphoPoint, PhosphoELM, Kinome, UNIPROT kinase, PHOSIDA, PhosphoNet, KEA.

For protein domains go to:
PDB, PawsonLab, Cell Signaling domains, CATH, CDD, SMART, Pfam, 3DID, InterPro, STRING, PPEP, DOMINO.

For gene ontologies go to:
GO database.

For enriched network analysis go to:
GeneCards, Enrichr, BioGPS, Panther.

For disease networks go to:
dSysMap, MalaCards, DISEASE, DisGeneNet, OMIM, GAD, Diseasome.

Go to the
Cytoscape Wall of Apps for a complete categorised list of all Cytoscape apps. Go here, for a Cytoscape plugins usage-chart and here for a dedicated review.

here for network topological analysis Cytoscape apps developed by the CBMC.

Go to
FastCentiscape for a web-based Centiscape-operated node centrality indexes computation of very large networks.

Go to
CentiServer for a comprehensive web-based resource for computation of network centrality indexes.

Go to
NeAT or a comprehensive web-based resource for network analysis.