The Mammalian Protein–Protein Interaction

Database and Its Viewing System That Is Linked to the Main FANTOM2 View

erGenome Research (2003)Genome Research (2003)

Speaker: Speaker: 蔡欣吟蔡欣吟Advisor: Advisor: 薛佑玲 老師薛佑玲 老師

IntroductionIntroduction

Protein – protein interaction database Protein – protein interaction database (PPI database)(PPI database)

The FANTOM2 viewerThe FANTOM2 viewer

FANTOMFANTOM

TheThe FFunctional unctional AnAnnonottation meeting ation meeting oof f mmouse cDNAouse cDNA The RIKEN Genome Exploration Research The RIKEN Genome Exploration Research

(GER) group(GER) group The RIKEN Mouse Gene Encyclopedia ProjeThe RIKEN Mouse Gene Encyclopedia Proje

ctct Determining the full coding potential of the Determining the full coding potential of the

mouse genomemouse genome FANTOM in 2000 to annotate first 21,076 cDFANTOM in 2000 to annotate first 21,076 cD

NAs NAs

FANTOM2FANTOM2

The second The second FFunctional unctional AnAnnonottation meation meeting eting oof f mmouse cDNA (2002)ouse cDNA (2002) The functional annotation of 60,770 full-leThe functional annotation of 60,770 full-le

ngth cDNAsngth cDNAs Provide the appropriate gene name, gene Provide the appropriate gene name, gene

symbol, coding sequence information, ansymbol, coding sequence information, and relevant gene ontology (GO)d relevant gene ontology (GO)

http://fantom2.gsc.riken.go.jp/http://fantom2.gsc.riken.go.jp/

The FANTOM2 viewerThe FANTOM2 viewer

RIKEN PPI DatabaseRIKEN PPI Database

InternalInternal Experimental PPI dataExperimental PPI data

External External DIPDIP BINDBIND FACTSFACTS

The DIP databaseThe DIP database

DDatabase of atabase of IInteracting nteracting PProteinsroteins

http://dip.doe-mbi.ucla.edu/http://dip.doe-mbi.ucla.edu/

The usage of DIPThe usage of DIP

StudyStudy Protein functionProtein function Protein-protein relationshipProtein-protein relationship Evolution of protein-protein interactionEvolution of protein-protein interaction The network of interacting proteinsThe network of interacting proteins The environments of protein-protein The environments of protein-protein

interactionsinteractionsPredictPredict Unknown protein-protein interactionUnknown protein-protein interaction The best interaction conditionsThe best interaction conditions

Current DIP Database Current DIP Database StatisticsStatistics

The BIND databaseThe BIND database

The Biomolecular Interaction Network Database

http://www.binddb.org/

What kind of data stored in BIND

INTERACTION: The interaction between two molecules as well as any chemical reactions that occur as a direct result of interaction. Example: P-P, P-n, P-s. (phosphorylation of P, methylation of

D, hydrolysis of sugar)

COMPLEX: describes a molecular complex by listing the series of interaction records that are present in the complex. Example: multi-sub enzyme, actin fiber, ribosome

PATHWAY: describes a cellular process pass a sequential list of interaction records and its associated Chemical Action data. Example: cell-signaling pathway, synthesis of an amino

acid, transcription and splicing of a pre-massager RNA.

Current BIND Database Current BIND Database StatisticsStatistics

The FACTS databaseThe FACTS database

FFunctional unctional AAssociation/Annotation ossociation/Annotation of cDNA f cDNA CClones from lones from TText/Sequence ext/Sequence SSourcesources

http://facts.gsc.riken.go.jphttp://facts.gsc.riken.go.jp

RIKEN PPI DatabaseRIKEN PPI Database

Reporter Gene

BaitProtein

BindingDomain

Prey Protein

ActivationDomain

Two hybrid proteins are generated with Two hybrid proteins are generated with transcription factor domainstranscription factor domains

Both fusions are expressed in a yeast cell that Both fusions are expressed in a yeast cell that carries a reporter gene whose expression is carries a reporter gene whose expression is under the control of binding sites for the DNA-under the control of binding sites for the DNA-binding domainbinding domain

The Two-Hybrid SystemThe Two-Hybrid System

Reporter Gene

BaitProtein

BindingDomain

Prey Protein

ActivationDomain

The Two-Hybrid SystemThe Two-Hybrid System Interaction of bait and prey proteins localizes Interaction of bait and prey proteins localizes

the activation domain to the reporter gene, the activation domain to the reporter gene, thus activating transcription. thus activating transcription.

Since the reporter gene typically codes for a Since the reporter gene typically codes for a survival factor, yeast colonies will grow only survival factor, yeast colonies will grow only when an interaction occurs. when an interaction occurs.

(BIND protein)(ACT protein)

The Protein-Protein The Protein-Protein Interaction DatabaseInteraction Database

The major part of PPIs in many PPI databThe major part of PPIs in many PPI database is yeast PPIase is yeast PPI The high number of false-positive interactionThe high number of false-positive interaction Data from two independent research groups Data from two independent research groups

showed very little overlopshowed very little overlop

The development of mammalian PPI dataThe development of mammalian PPI databasebase RIKEN PPI databaseRIKEN PPI database http://fantom21.gsc.riken.go.jp/PPI/http://fantom21.gsc.riken.go.jp/PPI/

FANTOM database

Get Clone IDGet Clone ID

Keyword search

Get clone ID

FANTOM database

Keyword search

Clone ID

FANTOM viewer

PPI

The RIKEN PPI DatabaseThe RIKEN PPI Database

AdvantageAdvantage The mammalian PPI databaseThe mammalian PPI database

ImprovementImprovement Need more dataNeed more data

Thank You for Your Attention