TUTORIAL From Protein-Protein Interactions (PPIs) to networks and pathways ???

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1 TUTORIAL From Protein-Protein Interactions (PPIs) to networks and pathways Dr. Javier De Las Rivas Dr. Carlos Prieto Bioinformatics and Functional Genomics Research Group Cancer Research Center (CIC - IBMCC, CSIC / USAL) Salamanca, Spain De Las Rivas & Prieto - Tutorial ISMB/ECCB - June high-throughput data produce masive networks --The high-throughput proteomic techniques are producig a masive amount of new data and PPI networks are becaming quite complex.??? De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

2 --- QA and QC of PPI data --There is a clear concern in this research area about the large amount of false positives produced both by the high-throughput proteomic techniques but also by many low-throughput small scale experiments published that have not been properly reported or properly curated. Therefore, PPI data need a proper Quality Assesment (QA) and Quality Control (QC).??? De Las Rivas & Prieto - Tutorial ISMB/ECCB - June Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --There is a clear concern in this research area about the large amount of false positives produced both by the high-throughput proteomic techniques but also by many low-throughput small scale experiments published that have not been properly reported or properly curated. Therefore, PPI data need a proper Quality Assesment (QA) and Quality Control (QC). Nature (2002) Mol. & Cell. Proteomics (2002) De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

3 Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --- BMC Bioinformatics (2006) Bioinformatics (2006) Proteins (2006) Nat. Biotech. (2004) Many attempts to gain confidence 5 Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --- Yu et al., Science (2008) completeness precision Cusick et al., Nature Methods (2009) New attempts to gain confidence Braun et al., Nature Methods (2009) based on experiments and unbiased HT De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

4 Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --- Key problems within the protein-protein interaction networks (from PPI networks to the interactome) 1.- Still partial >>> incomplete 2.- Many false positives >>> noisy 3.- Many inconsistent annotations >>> inaccurate 4.- Lack of cell-type-specific assignment >>> mixed (essential for metazoa: human, mouse, etc) Key problems - PPI networks incomplete - noisy - inaccurate - mixed ERROR De Las Rivas & Prieto - Tutorial ISMB/ECCB - June Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --- Key problems - PPI networks incomplete - noisy - inaccurate - mixed ERROR in 2008 known human proteome proteins (by intrg8, EBI) proteins involved in the human PPI from experimental data proteins (by APID, CIC) coverage 30.8 % Example of incomplete = Human PPI network De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

5 Protein-Protein Interactions (PPIs) --- QA and QC of PPI data --- Key problems - PPI networks incomplete - noisy - inaccurate - mixed ERROR Example of inaccurate = Lack of consistency between PPI DBs: BIND (Biomolecular Interaction Network Database) DIP (Database of Interacting Proteins) IntAct (Database system & analysis tools for PI data) De Las Rivas & Prieto - Tutorial ISMB/ECCB - June Protein-Protein Interactions (PPIs) --- improving PPI data --- We have developed a bioinformatic web platform to try to find consistency on the protein-protein interaction networks by unifiying well referenced experimental data. The tool is called APID and it allows full exploration of PPI information. APID (Agile Protein Interaction DataAnalizer) De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

6 Protein-Protein Interactions (PPIs) --- improving PPI data --- APID (Agile Protein Interaction DataAnalizer) BioGRID DIP HPRD MINT BIND IntAct At present 6 source PPI DBs were unified: BIND (Biomolecular Interaction Network DB) BioGRID (Biological Gral. Repository for Interaction Datasets) DIP (Database of Interacting Proteins) HPRD (Human Protein Reference Database) IntAct (Database system & analysis tools for PI data) MINT (Molecular Interactions Database) Data integration and unification by Sequence UniProt_ID PubMed_ID De Las Rivas & Prieto - Tutorial ISMB/ECCB - June Protein-Protein Interactions (PPIs) --- improving PPI data --- APID data integration and data unification by Sequence UniProt_ID PubMed_ID 12

7 Protein-Protein Interactions (PPIs) --- integration & unification of PPI data --- APID (Agile Protein Interaction DataAnalizer) ppi 22.5 % MINT 1017 ppi 1.75 % DIP ppi 40.9 % BioGRID ppi 63.3 % HPRD in 2008 human proteins proteins human interactions interactions BIND 9.66 % 5626 ppi IntAct 34.9 % ppi in 2007 human interactions interactions in 2008 human interactions interactions De Las Rivas & Prieto - Tutorial ISMB/ECCB - June integration & unification of PPI data --- Exploring the data of 2 major papers that applied high-throughput two-hybrid techniques to map the human interactome RUAL et al., Nature (2005) STELZL et al., Cell (2005) De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

8 --- integration & unification of PPI data --- Exploring the data of 2 major papers that applied high-throughput two-hybrid techniques to map the human interactome RUAL et al., Nature (2005) 1526 prot by Y2H (APID) STELZL et al., Cell (2005) 1665 prot by Y2H (APID) Only 294 proteins in common HUBs marked De Las Rivas & Prieto - Tutorial ISMB/ECCB - June integration & unification of PPI data --- Exploring the data of 2 major papers that applied high-throughput two-hybrid techniques to map the human interactome APID RUAL STELZL PA1B2 LRSM1 CDN1A ADT3 TCEA2 SGTA RGS2 RAB1A PP16A MARK3 CCD53 PSME3 PHC2 DVL3 PIN1 ZNF24 PRAF1 UBC9 MOB3 ARI2 MYST2 NRIF3 PA1B3 DAZP2 UT14A BAT3 P53 TRP13 ZBT16 SAT1 VIME EF1G UN119 MDFI 40 proteins most highly connected (>25 ppi) (for APID: include only the interactions by Y2H method) PSA1 NCK2 HSP7C EPS8 TTHY TBC17 De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

9 --- unified PPI data with Q-filters --In APID_2H: 1169 human proteins and 6237 pair-wise interactions (proven by 1 method) PPI network 1169 prot 6237 inter InterPro kinases 149 prot IPR IPR prot_kinase kinase_like GO-BP signal transduction 171 prot GO: unified PPI data with Q-filters --In APID_2H: 1169 human proteins and 1787 pair-wise interactions (proven by 2 methods) PPI network 1169 prot 1787 inter InterPro kinases 119 prot IPR IPR prot_kinase kinase_like GO-BP signal transduction 136 prot GO:7165 De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

10 --- unified PPI data with Q-filters method 2 methods 2 methods + ipfam indirect validation --- conclusions It is important to define well what is a protein-protein interaction (PPI) to avoid confusion with other types of biomolecular relationships or associations. 2.- PPI networks are scale free networks with different types of hubs that are critical nodes with specific topological characteristics. 3.- The two major high-throughput methods to find PPIs are: tandemaffinity purification and mass spectrometry (TAP-MS) and two-hybrid systems (2H). These methods provide quite different mapping of PPIs because TAP-MS is complex oriented but 2H is binary oriented. 4.- Due to the large proportion of false positives and the low overlapping of PPI data from diferent source databases, a major effort is needed in quality assessment (QA) and quality control (QC). Data integration and unification, including reference sets and scoring schemes is a good approach to achieve PPI data improvement. De Las Rivas & Prieto - Tutorial ISMB/ECCB - June

11 --- conclusions The analyses of PPI networks allow to find clusters of nodes highly interconnected, that usually can be assigned to specific molecular machines like the proteasome. These clusters include a kind of critical nodes or hubs that have been called: intramolecular hubs. 6.- The analysis of PPI networks allow to find other type of critical nodes or hubs that are highly connected with many nodes that show low interconnection. These hubs can be usually assigned to molecular regulators included in pathways, like the signal transducers. These critical nodes that have been called: intermolecular hubs. De Las Rivas & Prieto - Tutorial ISMB/ECCB - June examples for the practicals of the tutorial A molecular machine: PROTEASOME, complex interaction and a clear subnetwork 2. A signaling pathway: NOTCH, integration of the pathway and the PPI network 3. Building a molecular machine: Pre-RIBOSOME, steps for its biogenesis and assemble De Las Rivas & Prieto - Tutorial ISMB/ECCB - June