Analysis and visualization of protein-protein interactions. Olga Vitek Assistant Professor Statistics and Computer Science

Transcription

1 1 Analysis and visualization of protein-protein interactions Olga Vitek Assistant Professor Statistics and Computer Science

2 2 Outline 1. Protein-protein interactions 2. Using graph structures to study protein-protein interactions 3. Clustering of graphs 4. Evaluation of clusters

3 3 An Introduction to Bioinformatics Algorithms "#$%&$'"()%*"+,%-$.. A cell is a smallest structural unit of an organism that is capable of independent functioning All cells have some common features

4 4 An Introduction to Bioinformatics Algorithms "#$%&"#$%'()%*+,%-./0%/1 2(1/34'*5/( Replication Transcription Translation This model is known as the central dogma

5 Why should we study proteins? Ubiquitin-conjugating enzyme E2 G1 (PDB entry 2AWF) 5 Proteins: large molecules made up of amino acids accomplish most of the function of the living cells by interacting (i.e. entering in physical contact) with other molecules linear structures fold into 3-dimensional shapes the structure is used to accomplish the function

6 6 Proteins accomplish function by forming complexes A protein complex is a group of tightly interacting proteins also called functional module protein interactions within the complex help accomplish its function Example: exosome a complex of 11 proteins degrades RNA molecules ring structure ensures the function

7 7 Discovery of the complex helps understanding its function Example: exosome first discovered in yeast helped discovering an equivalent complex in humans has clinical implications target of autoimmune disease chemotherapies for cancer block its activity Knowledge of protein complexes speeds up biological and clinical research

8 8 Complexity of a bacterial cell Often study simpler model organisms to gain insight into the function of the cell

9 9 Modern technologies determine protein interactions on large scale New terms Proteome: all proteins that exist in an organism Interactome: all protein-protein interactions New questions Interactions of individual proteins Network-wide patterns of interactions New challenges Large, complex, noisy datasets Computational approaches are key

10 10 B I N D DNA damage response and repair DNA metabolism DNA recombination DNA replication RNA localization and processing autophagy budding carbohydrate metabolism cell cycle cell growth and/or maintenance cell organization and biogenesis cell shape and cell size control general metabolism mating nucleolar and ribosome biogenesis protein amino acid phosphorylation/desphosphorylation protein biosynthesis protein degradation protein metabolism and modification protein transport signal transduction sporulation stress response transcription transport Kss1 Bck2 Ste7 Dig1 Ste12 Ste11 Bem3 Ylr154c Rvb1 Aco1 Rvs167 Ded1 Gyp5 Ecm29 Hom6 Ilv5 Lys12 Pho84 Pre10 Ubp7 Ura7 Met18 Ylr243w Ubi4 Idh1 Apg12 Crm1 Fet3 Kap122 Kgd1 Met10 Pfk1 Rpn1 Car1 Hyp2 Ipp1 Mdh1 Cnb1 Cmp2 Cns1 Ecm10 Yhb1 Cof1 Crn1 Srv2 Hta1 Hhf1 Hir2 Htb1 Kap114 Kri1 Nap1 Nop4 Ret1 Rpc82 Rpo31 Spt16 Rrp13 Ylr222c Cct2 Cys4 Dig2 Pim1 Rpa135 Rpn6 Tec1 Yer093c Ygl245w Yjr072c Yol078w Lsm8 Apa1 Gar1 Lsm2 Qcr2 Rpn12 Rpn8 Rrp42 Smb1 Tif6 Ygl117w Mig1 Mss116 Nop12 Nop2 Brx1 Ckb1 Cox6 Fet4 Nsa2 Nip7 Nmd3 Nop1 Rrp1 Sik1 Nug1 Nsa1 Noc2 Ypl009c Rpc19 Rpn5 Emp24 Kre6 Rpn9 Rpt1 Rpt2 Sip2 Arc35 Gal83 Idh2 Sec53 Snf1 Snf4 Tcp1 Smt3 Cpr1 Gph1 Pst2 Rod1 Sip1 Yor267c Spo12 Pse1 Tem1 Cdc15 Gcd11 Mcx1 Sar1 Ybr281c Yhr033w Ynk1 Ubc6 Atp4 Gcn1 Los1 Pol5 Sec7 Uba1 Ybl004w Ykl056c Ypt1 Yju2 Cor1 Ded81 Prp19 Dss4 Gdi1 Mrs6 Sec4 Cdc53 Por1 Skp1 Ela1 Loc1 Yra1 Cic1 Glc7 Glc8 Mhp1 Reg1 Kap104 Ynl035c Dim1 Enp1 Nab2 Hrp1 Mrt4 Prp6 Hsl7 Rpp0 Ylr287c Fyv14 Krr1 Yjr041c Rpf2 Kre33 Tsr1 Tif4631 Drs1 Erb1 Ydr131c Yrb2 Yhr197w Arf1 Arf2 Cmd1 Cmk2 Ede1 Myo2 Myo4 Myo5 Pgm2 Vas1 Vps13 Ils1 Sod1 Hch1 She3 Dmc1 Est1 Puf6 Rrp12 Cbf5 Dbp7 Hsh49 Pet56 Pdi1 Pwp1 Yer077c Yjl109c Ykl014c Fpr1 Hom3 Gsp1 Gsp2 Srm1 Rna1 Mog1 Rse1 Ist3 Bud13 Car2 Ssz1 Ydr341c Sah1 Lsm7 Pat1 Ade5 Dhh1 Lsm4 Prp24 Met30 Rub1 Sis1 Tef4 Met4 Met31 Nop13 Ebp2 Imd2 Imd3 Rrp5 Rad10 Rad1 Sod2 Ubc1 Adk1 Yhr115c Ynl311c Ypt6 Ric1 Cdc11 Cdc3 Cdc10 Cdc12 Tif4632 Ctf13 Hrt1 Rtt101 Sec27 Guf1 Yll034c Tps1 Ubp15 Rpc40 Rpa190 Sgn1 Ygr250c Spt2 Cka1 Cka2 Ygr052w His4 Gpi16 Cdc42 Bem4 San1 Gbp2 Hpr1 Sub2 Thp2 Mft1 Rlr1 Rho2 Ubc12 Ula1 Clb2 Cdc28 Dia2 Cks1 Hat1 Vps21 Ypt10 Ypt52 Ypt32 Ypt31 Ypt7 Gpa2 Ymr029c Grr1 Pfk2 Pfs2 Rpt3 Ygl004c Rpn10 Snp1 Bcy1 Tpk3 Tpk1 Sti1 Ypt53 Cce1 Rnr3 Cmk1 Vph2 Cpr6 Qns1 Trr1 Caf120 Ptc4 Ydr247w Gin4 Ydr071c Mas1 Mas2 Gis4 Prb1 Sxm1 Ecm1 Lhp1 Yjl149w Cdc13 Fun11 Clu1 Tif2 Gnd1 Kip3 Hef3 Inp52 Sap190 Nta1 Hsp104 Vma4 Tfp1 Mge1 Ptc5 Yal027w Spo13 Ydr219c Yhr122w Ydr306c Yku80 Msu1 Ylr352w Yol128c Oye2 Bur2 Cln1 Clb5 Clb3 Yer138c Ydr170wa Nup85 Hem15 Ymr209c Cbp3 Nup84 Seh1 Pre1 Pup2 Pup3 Ylr199c Pre5 Pre2 Pre3 Pre6 Pre7 Scl1 Ykl206c Pre9 Pre8 Rsp5 Rvs161 Bop2 Sgt1 Ufo1 Cdc4 Yil007c Yta6 Ygr086c Ypl004c Top2 Cdh1 Cct3 Cat5 Yjl068c Gyp6 Trs120 Trs130 Rpb5 Rpa43 Ybr203w Yck1 Yck2 Ypr015c Bud20 Ydr101c Prp43 Rsm25 Afg2 Fyv4 Ypl013c Rsm24 Yjl122w Ybl044w Nog1 Ydr036c Htb2 Mam33 Ygl068w Cdc23 Swm1 Cdc5 Mcd1 Smc1 Gsy1 Fpr3 Sds22 Fin1 Gpa1 Hex3 Ssk1 Hrr25 Prp3 Prp4 Ymr226c Apc1 Nop58 Ygr145w Kap95 Cbp2 She4 Mlc1 Nuf1 Hul5 Myo3 Faa4 Rnq1 Ydr279w Ado1 Lsm1 Ygr173w Ydr152w Ykl078w Ylr097c Adh2 Imd4 Pet127 Tis11 Ytm1 Yrb1 Gal3 Bbc1 Cdc39 Mms1 Pma2 Yar009c Ygp1 Ylr035ca Ylr106c Adr1 Mkt1 Dur1 Ecm33 Hsp12 Sec26 Qri8 Ahp1 Dop1 Sry1 Rvb2 Npl3 Pub1 Fun12 Ste23 Ssf1 Aac3 Kre31 Rli1 Srp1 Sup45 Ygr090w Tpt1 Apc2 Mak5 Ynl116w Dbf2 Mob1 Ess1 Tfg1 Rpo21 Tom1 Spt5 Hxt6 Rpb3 Ynl253w Isu1 Nfs1 Lys1 Fol2 Tal1 Cct5 Cct6 Cft1 Hgh1 Mer1 Lhs1 Rpn3 Rpn7 Rpt5 Nas6 Arp2 Rpt4 Rpn11 Cpr3 Cdc33 Dut1 Ygr066c Thi22 Tpk2 Ybr028c Yck3 Ygr154c Ssn8 Sno2 Ygr111w Yjl207c Yil113w Slt2 Ynl260c Asi3 Ypl170w Pma1 Ynl227c Cdc14 Mcr1 Dpm1 Atp7 Atp5 Fur1 Hms1 Ydr453c Atp3 Spe3 Aut2 Spc72 Ydr229w Irr1 Smc3 Faa1 Cyr1 Dbf20 Ala1 Egd2 Axl1 Rpb10 Dbp8 Cpa2 Rnr1 Rnr2 Ydl086w Pdc6 Pdc5 Ynl157w Prs5 Dia4 Bud32 Grx4 Ykr038c Yml036w Isw2 Isw1 Kns1 Msg5 Fus3 Msh1 Pph22 Cdc55 Ppe1 Rts1 Tpd3 Ygr161c Hta2 Ygl121c Rpb11 Tap42 Pro1 Arc1 Fum1 Rad51 Mlh1 Tos3 Ykr096w Yak1 Dnm1 Vps1 Ylr270w Ypl247c Mpc54 Yhr112c Pyc2 Ybl108w Oye3 Ycr079w Vid31 Cdc60 Pro2 Pyc1 Ypl110c Ykl215c Emg1 Yer030w Ynl099c Siw14 Ypk2 Pet112 Ygr016w Yel023c Yor154w Yor220w Rad3 Dun1 Far1 Gpd1 Gpd2 Sen1 Ste20 Sec6 Ylr368w Rad26 Ach1 Adh4 Bio3 Erg20 Yhr076w Ymr318c Rhr2 Ydr326c Ras2 Ras1 Acc1 Gfa1 Isa2 Ngl2 Rpa49 Rpc25 Rpo26 Tbs1 Yfl042c Rpc34 Sen15 Egd1 Erg13 Erg6 Frs2 Gnd2 Grx1 Aat2 Afr1 Lro1 Met6 Ntf2 Prm2 Rsn1 Scp160 Ses1 Snu13 Ths1 Vma5 Wtm1 Ybr025c Dog1 Has1 Prp8 Sap185 Sit4 Ylr386w Yhr214wa Ydl025c Yal049c Yhr009c Apt1 Aro1 Ydr128w Ylr238w Erg1 Cdc7 Bfr2 Bir1 Nut1 Thi3 Ylr231c Ylr331c Bms1 Cdc46 Ctf4 Dbp10 Lst4 Mcm2 Mcm3 Spb1 Ssf2 Ybl104c Pph3 Ybl046w Ynl201c Prp11 Cop1 Nan1 Rex2 Shm2 Ssk2 Bck1 Gal7 Kic1 Kin2 Mkk2 Smk1 Ydr214w Ylr187w Gdb1 Rad50 Ubr1 Ylr241w Yor173w Ykl161c Ynl056w Yol045w Fun30 Fun31 Aac1 Apg17 Cvt9 Ppx1 REP1 Sec18 Tyr1 Yhr020w Ynl208w Yor086c Grx3 Idp2 Pho81 Sec23 Yor073w Dog2 Msk1 Rgd1 Vma22 Aip1 Arp7 Mse1 Ydr239c Ypr115w Rad54 Ynl134c Cdc9 Dbp9 Pol30 Yor378w Sld2 Trl1 Lif1 Dnl4 Mec3 Mak16 Ydr198c Ygl146c Nop15 Mlh3 Pso2 Mgm101 Rad2 Pex15 Mre11 Vma8 Xrs2 Rad7 Elc1 Rfa2 Hir3 Ubc13 Aro9 Mms2 Rad18 Whi2 Csr2 Tdp1 Shp1 Yen1 Fpr4 Lcd1 Adh5 Mag1 Ai1 Hho1 Hht1 Mph1 Msh2 Yor155c Mus81 Anc1 Cdc16 Mes1 Mms4 Nhp2 Rad53 Rpc10 Yer078c Ntg1 Rfc2 Tif34 Rad24 Rfc3 Rfc5 Ylr413w Asf1 Ptc2 Swi4 Tbf1 Ymr135c Yta7 Rad59 Bem2 Hor2 Ilv2 Opy1 Pgm1 Ptc3 Rad52 Rad9 Rfa1 Rfa3 Hxt7 Yjr141w Brr2 Rfc4 Rom2 Vac8 Sml1 Adh3 Nat1 Dpb11 Hpr5 Phr1 Msd1 Pol4 Rho5 Rad16 Htz1 Pdx1 Rad30 Map2 Ycl042w Efd1 Rfc1 Rhc18 Imd1 Set1 Bre2 Trf4 Mtr4 Ydl175c Yil079c Ypl146c Ddc1 Suv3 Rad17 Mgt1 Rip1 Sof1 Ira2 Rad14 Rad4 Rad28 Ccl1 Kin28 Lsc1 Tfb3 Ybr184w Ald5 Bul1 Lsb1 Ykr018c Ylr392c Sir3 Gas1 Sir1 Ubp8 Sir4 Blm3 Sir2 Yfl006w Yku70 Pex19 Arc15 Arc18 Arc19 Arc40 Arp3 Puf3 Fhl1 Fkh1 Fkh2 Gcn3 Hmo1 Ceg1 Ckb2 Fyv8 Gcd2 Gcd7 Mbp1 Net1 Sec2 Sin3 Sui2 Sui3 Ubp12 Ure2 Ygr017w Ymr144w Ino80 Lap4 Ams1 Bik1 Pib1 Pph21 Prk1 Abp1 Akl1 Dis3 Eaf3 Fip1 Nam8 Nup1 Nup2 Nup60 Pap1 Pct1 Reb1 Rnt1 Rrp4 Rrp43 Rrp6 Rtt103 Sif2 Snu56 Sto1 Tra1 Ume1 Ypr090w Fal1 Gcd1 Gcd6 Ubc4 Qcr7 Ufd4 Ydl100c Ybr014c Yer083c Ygl020c Ydr200c Yfr008w Yol054w Gac1 Pob3 Ycr030c Yor056c Ypr093c Rpb9 Rgp1 Hts1 Apm3 Apl5 Las17 Bzz1 Gal2 Pep1 Sla1 Sqt1 Vma6 Vrp1 Yhm2 Ynr065c Pds1 Pkh2 Ygr033c Cef1 Clf1 Snt309 Ygr205w Sat4 Pho85 Ydr516c Ygr165w Num1 Sef1 Skt5 Syf1 Ygl081w Nip1 Gsy2 Ylr016c Smc4 Ynl094w Ypl150w Aro4 Cbk1 Sgt2 Ssd1 Gip2 Hal5 Itr2 Kin82 Ynr047w Ksp1 Chs1 Pri2 Yhr186c Lem3 Nmd5 Yhr199c Ylr326w Ppq1 Yhl010c Nha1 Ybl049w Ykr017c Trx2 Usa1 Pex6 Chk1 Ctr1 Ssk22 Bud7 Mae1 Bfa1 Nup53 Ybr063c Dpb2 Lst8 Pho86 Srp54 Ykr051w Ylr271w Yml020w Ypr003c Rrp3 Slc1 Tfc7 Ygr266w Nog2 Met16 Slx1 Ybt1 Ynl040w Bmh1 Bnr1 Boi2 Kcs1 Nth1 Yfr017c Yil028w Cyk3 Sok1 Stu1 Svl3 Caf4 Ent2 Ybl029w Osh7 Sap1 Pex7 Fzo1 New1 Rrp9 Rtf1 Spt7 Ate1 Epl1 Mpt1 Vid21 Arp4 Esa1 Tuf1 Sdf1 Yel064c Snt1 Trm3 Yil112w Ylr409c Ymr155w Yrf1-3 Zds2 Wtm2 Swd3 Sfp1 Sgs1 Ydr316w Bud9 Dak2 Kin1 Ynl182c Q0032 Bub3 Q0092 Rpf1 Ypd1 Vps35 Ybr242w Yil137c Sec28 Ypl222w Bud3 Cin8 Hir1 Mak11 Mck1 Pnt1 Yil105c Msi1 Set3 Pkh1 Prp46 Cdc54 Ypl113c Sap155 Eap1 Ybr187w Ycr076c Ykr007w Btn2 Hxt5 Swe1 Ahc1 Kel1 Tep1 Mlp2 Tup1 Cyc8 Ssy5 Sph1 Ydl156w Rpl23b Bcp1 Ypl208w Rpn13 Pol2 Ygl104c Noc3 Yhl035c Hot1 Ydr116c Ykl082c Cna1 Ygr263c Ctk1 Cdc37 Hrb1 Elp2 Elp3 Jip1 Iki3 Zms1 Hat2 Hif1 Hog1 Rck2 Pac11 Ybl064c Dyn2 Pbs2 Pps1 Ade13 Ppz2 Yor054c Pwp2 Ygr210c Sec13 Sec31 Nup133 Yhl039w Las1 Yor283w Ycl039w Ydr255c Vid28 Fyv10 Vid30 Yer066ca Ygr223c Erg10 Yjr061w Kkq8 Yjl069c Arp10 Dip2 Dip5 Mum2 Yil055c Bmh2 Cln2 Gcn2 Ynl213c Pop2 Tfc4 Kel2 Bud14 Mih1 Pac2 Ydr449c Ygr130c Nsr1 Sul2 Ydr267c Ubp9 Yol111c Ygl131c Yor353c Ctk3 Stb3 Fap1 Mek1 Pcl9 Psr1 Ser1 Ufd2 Tsl1 Dsk2 Hmf1 Ydr049w Npl4 Rad23 Ylr247c Exo70 Cin5 Ymr291w Vps33 Ypl236c Hym1 Yfr039c Ltp1 Mot1 Mob2 Pcl6 Rpg1 Top1 Yfr011c Yol087c Tif35 Yor227w Aut10 Apg2 Ptc1 Ris1 Apg7 Ape3 Yml072c Cpa1 Prp28 Rpd3 Ydr266c Ymr093w Rok1 Are2 Bre1 Yhr149c Ypl055c Ime4 Pep3 Ymr086w Sum1 Lsb3 Yfr024c Prp12 Ylr422w Yor042w Yjl045w Ygr280c Cik1 Elm1 Scd5 Ydr412w Ptp2 Ydl063c Dps1 Msn5 Gal11 Prp31 Skm1 Hmg2 Swd1 Ygr067c Yir003w Rlp24 Gpi15 Yhr046c Bub2 Ism1 Ylr152c Dcp2 Crz1 Dcp1 Sfb3 Tgl1 Ybr225w Sgm1 Mds3 Pin4 Sas10 Yel015w Ynl207w Rpm2 Cdc25 Ltv1 Yor215c Mec1 Rad27 Yhr196w Tps2 Scs2 Mms22 Esc4 Gdh2 Arl3 Chd1 Mlc2 Prs3 Ira1 Rpa12 Yer067w Yhr087w Ura3 Isa1 Ygr150c Ygr198w Red1 Rim11 Gcr2 Yjr028w Cki1 Pmd1 Prs2 Yer160c Yjr027w Ybr094w Ybr267w Ydr339c Pmc1 Ydr365c Ynr054c Ycr087w Ydr102c Yfr003c Yfr016c Cap2 Cap1 Ylr427w Are1 Msc3 Grs1 Swi1 Kex2 Tao3 Ccr4 Cdc36 Yer084w Dbp2 Osh3 Ptp3 Swi5 Stb4 Faa2 Hfi1 Ygr002c Tel1 Ybr280c Ybr139w Aah1 Ycr001w Yfl034w Ypr143w Yhr105w Ssq1 Mub1 Spb4 Ubr2 Sth1 Ysc84 Scp1 Sps1 Apm1 Shs1 Gcn5 Ada2 Taf60 Sgf29 Hap2 Cis1 Ykl214c Ypr085c Hap5 Ypl166w Nop16 Ynl063w Grh1 Hap3 Mdh2 Exg1 Yil108w Med4 Zrg17 Psr2 Ssl2 Rad55 Rck1 Rim15 Rlf2 Ygl060w Ski8 Ski2 Ski3 Sln1 Taf90 Prp40 Ykl099c Yml093w Ykr060w Yor145c Lcp5 Caf20 Cdc20 Mad3 Cse2 Ime2 Sdh2 Ydr372c Ykr046c Ste4 Ybl036c Ydl193w Ydr482c Ygr054w Ino4 Ydr324c Msh3 Ygl220w Yll029w Yjr110w Rgr1 Yfl030w Pcl7 Efb1 Kgd2 Krs1 Pmi40 Lpd1 Arg1 Trp5 Ara1 Thr4 Sac6 Ape2 Pab1 Mdh3 Acs2 Hom2 Ydl124w Bat1 Gcy1 Ade6 Cys3 Ade3 Ura1 Rho4 Msn4 Van1 Mnn9 Bni1 Cdc47 Yjr029w Trp3 Imh1 Pdx3 Thi21 Ade17 Ymr145c Ktr3 Nop14 Mdj1 Cvt19 Dld3 Cdc123 Sui1 Arg4 Rho1 Yfr044c Ilv3 Apg5 Ymr315w Ymr102c Afg3 Tfg2 Bgl2 Cbp6 Psd1 Oac1 Pet9 Ayr1 Pro3 Scw4 Msh6 Yil104c Ymr323w Pda1 Nbp2 Ppz1 Snu66 Sks1 Nup145 Ctf19 Ypl181w Gsf2 Spc24 Glt1 Spc25 Ymr196w Rmt2 Yjr070c Sen2 Asc1 Trp2 Rcl1 Apl2 Ylr328w Apl4 Pib2 Rlp7 Apm4 Rad6 Yjl107c Sec21 Erg27 Gpt2 Ynl181w Ydl204w Om45 Ret2 Yer049w Ydr398w Sgd1 Pox1 Npr2 Yer182w Vps8 Ydr233c Vid24 Yor172w Cac2 Ydl113c Ynl124w Sac1 Wbp1 Hsm3 Rpl5 Nup120 Vps41 Crc1 Figure S3: View of the entire HMS-PCI Dataset. Thick blue lines represent literature-derived interactions from PreBIND+MIPS in the HMS-PCI dataset. Thin orange lines represent potential novel interactions. Arrows point from bait to associated protein. Functional annotation derived from Gene Ontology.( Ho et al., Nature, 2002 New technologies determine proteinprotein interactions on a large scale Such datasets are being increasingly produced, and are publicly available

11 11 Outline 1. Protein-protein interactions 2. Using graph structures to study protein-protein interactions 3. Clustering of graphs 4. Evaluation of clusters

12 12 Representing protein-protein interactions using graphs Interaction attributes: type confidence direction experimentally determined interaction protein A protein B Protein attributes: name function quantitative data Protein attributes: name function quantitative data

13 13 Representing protein-protein interactions using graphs Interaction attributes: type confidence direction experimentally determined interaction Experimental artifact protein A protein B Protein attributes: name function quantitative data Protein attributes: name function quantitative data

14 14 Representing protein-protein interactions using graphs Use graphs to represent the large-scale information on proteins, interactions and their attributes

15 Graph-based representation 15 of protein-protein interactions Ste4 Wtm1 Akl1 Psr1 Ynl094w Cdh1 Nip1 Aat vt19 9c Cln1 Yol111c Rgd1 Rrp42 Ilv3 Ubp7 Ste12 Apa1 Gis4 Aro1 Arp3 Ybr280c Pcl9 Sph1 Arc35 Rpa49 Ynl201c Bul1 Tup1 Ppq1 Yjr141w Ski8 Met10 Ski2 Yfr044c Caf20 Trp2 Nsr1 Esc4 Arf1 Cdc3 ce DNA DNA met DNA recomb DNA replication general metabolism mating nucleolar and ribosome bio protein amino acid phosphorylat protein biosynthesis protein degradation Ubr1 Cdc23 Ach Ygr130c Bck1 Pkh2 Yil113w Pdx3 Whi2 Mms22 Rad9 R View data as a graph Proteins are nodes and interactions are edges Nodes have attributes e.g. known function Directed edges experimental artifact

16 The interactions are determined 16 by tag-affinity purification (TAP) a 1 Tag b c Bait Isolate protein complex 5 SDS PAGE Affinity column A protein ( bait ) is labeled by a chemical The bait forms its interactions (collects prey ) The bait, and all other proteins in the complex are isolated d Protein 1 Protein 2 Protein 3 Protein 4 Protein 5 Excise bands Digest with trypsin Analyse by mass spectrometry and bioinformatics All components of the complex are identified by mass spectrometry Kumar & Snyder, Nature, 2002

17 The interactions are determined 17 by tag-affinity purification (TAP) prey Tag bait KLNFMTP... protein complex PNGFLKK... SRKNFSL... KFWQTY... KKRLMTP... cell 1. Tagging 2. Purification 3. Identification

18 The technology yields false positive and false negative interactions 18 tag Can not distinguish between various types of complexes chain star complete graph Use the spoke model to represent results of experiments directed edges from bait to prey multiple proteins in a complex can be used as a bait direction of edges reflects experimental design, but not the underlying biology bait spoke prey

19 19 Global graph-based summaries: degree of a node Each node is labeled with its degree Degree of a node: the number of edges that the node has to other nodes degree distribution: fraction of nodes in the network with a different degree mean degree: average degree over all nodes

20 20 Degree distribution: Gavin et al., 2002 Node Count Degree Only a few nodes have a large number of edges

21 21 Global graph-based summaries: clustering coefficient Clustering coefficient of a node: the fraction of the neighbors of a node that are also neighbors Clustering coefficient of a network: average clustering coefficient over all neighbors

22 22 Mean degree vs clustering coefficient of experimental networks Krogan2004 Clustering coefficients Tong2002 Hazbun2003 Ho2002 Uetz2000 Li2004 Ito2001 Stelzl2005 Gavin2002 Gavin2006 Krogan Mean degree APMS Y2H Two technologies: tag affinity purification yeast-twohybrid

23 23 Conclusion from these summaries for protein interaction networks: Most nodes have a low degree (i.e. few neighbors) Some nodes have a high clustering coefficient (i.e. their neighbors are also neighbors) Of interest are protein clusters (i.e. groups of proteins that interact with each other more closely than outside the group) close interactions can help infer biological function challenge: large and noisy datasets

24 24 Outline 1. Protein-protein interactions 2. Using graph structures to study protein-protein interactions 3. Clustering of graphs 4. Evaluation of clusters

25 Our goal: find protein clusters in the 25 large and noisy interaction graph Gavin et al., Nature, 2002

26 26 Step 1: de-noise the interaction graph We are more confident in protein interactions if they are determined using multiple baits remove isolated subgraphs determine connected components subgraphs where there is a directed path from each protein to every other protein Gavin et al., Nature, 2002

27 27 Step 1: de-noise the interaction graph We are more confident in protein interactions if they are determined using multiple baits remove isolated subgraphs determine connected components subgraphs where there is a directed path from each protein to every other protein Isolated component Gavin et al., Nature, 2002

28 Step 2: based on the graph topology, 28 find protein clusters in the connected components Finding clusters ignore directions of edges use Markov Cluster (MCL) algorithm for clustering The output are sets of closely interacting proteins Not every protein is expected to cluster Gavin et al., Nature, 2002

29 Step 2: based on the graph topology, 29 find protein clusters in the connected components Output of a clustering procedure Exosome example: additional proteins were found by clustering the network Gavin et al., Nature, 2002 Gavin et al., Nature, 2006