Assignment 1Assignment 5 • Write a script which can calculate the degree and clustering coefficient...

Question

Assignment 1Assignment 5 • Write a script which can calculate the degree and clustering coefficient for every node (protein) in the human protein interaction network (attached).  Now calculate the average clustering coefficient of the network. Finally,  test whether the network has a scale-free structure by plotting the degree distribution ?• Now write another script which can calculate the shortest path lengths between every pair of nodes (proteins) in the attached files (two files are attached). Compare the path length distributions between the two protein sets using a wilcox test.  OFFICIAL_SYMBOL_A       OFFICIAL_SYMBOL_B1810055G02Rik    MPRIP1810055G02Rik    RAI141810055G02Rik    TPM12810046L04Rik    ARF12810046L04Rik    ARF34922501C03Rik    CPNE44930572J05Rik    C8orf554930572J05Rik    PRKDC4930572J05Rik    SPRR2B4930572J05Rik    SPRR2D4930572J05Rik    SPRR2E4930572J05Rik    SPRR2G9830001H06Rik    C1QBP9830001H06Rik    CCDC1659830001H06Rik    DYNLL19830001H06Rik    KIAA08899830001H06Rik    PPP2CA9830001H06Rik    PPP2R1A9830001H06Rik    PPP2R5A9830001H06Rik    PPP2R5E9830001H06Rik    RNF41A1CF    APOBEC1A1CF    KHSRPA1CF    SYNCRIPA2M    ADAMTS1A2M    APOEA2M    IL10A2M    IL4A2M    LCATA2M    LEPA2M    NGFA2M    PAEPAAGAB    EIF3CAATF    CHEK2AATF    MAGED1AATF    MAPTAATF    PAWRAATF    PCBD2AATF    RB1AATF    RBL1AATF    RBL2AATF    RELAAATF    Tsg101ABCA1    AOX1ABCA1    APOA1ABCA1    CDC42ABCA1    COPS5ABCA1    CREBBPABCA1    FADDABCA1    FLOT1ABCA1    HGSABCA1    PRPF8ABCA1    SDHBABCA1    SNTB2ABCA1    STX12ABCA1    UBCABCA1    UGP1ABCA1    XPCABCA13    APOA1ABCA13    APOA2ABCA2    CDK5RAP2ABCA4    CNGB1ABCB1    DHX9ABCB1    PIM1ABCB1    UBCABCB7    FECHABCC2    PDZD3ABCC2    RdxABCC2    SLC9A3R1ABCC8    KCNJ11ABCC8    RAPGEF4ABCD1    ABCD2ABCD3    ABCD1ABCD3    PEX19ABCD4    PEA15ABCD4    XRCC6ABCE1    RNASELABCE1    UBASH3AABCF3    ACIN1ABCF3    DNALI1ABCF3    LAMTOR1ABCF3    TOE1ABCG1    UBCABCG5    ABCG8ABHD16A    ATP5G3ABHD16A    DNAJC1ABHD16A    GPRC5CABHD16A    HM13ABHD16A    IFITM1ABHD16A    RNF5ABHD16A    SAFBABHD16A    SPAG7ABHD16A    TMEM147ABHD16A    TMEM222ABI1    ABL1ABI1    ENAHABI1    EPS8ABI1    NCK1ABI2    ABL1ABI2    CCDC53ABI2    IFT20ABI2    KRT20ABI2    TRIM32ABI2    UBCABI3    ABI3BPABI3    CEP170P1ABI3    CEP44ABI3    DTNBP1ABI3    PAK1ABI3    PAK2ABL1    ABI1ABL1    ABI2ABL1    ABL1ABL1    ABL2ABL1    ATMABL1    ATRABL1    BAG1ABL1    BCAR1ABL1    BCRABL1    BRCA1ABL1    CATABL1    CBLABL1    CREB1ABL1    CRKLABL1    Creb1ABL1    DOK1ABL1    EPHA3ABL1    EPHB2ABL1    EVLABL1    GPX1ABL1    GRB10ABL1    GRB2ABL1    HCKABL1    HSP90AA1ABL1    HSPA4ABL1    INPPL1ABL1    JAK1ABL1    Jak1ABL1    MDM2ABL1    MICAL1ABL1    MTORABL1    NCK1ABL1    NCOA3ABL1    NEDD9ABL1    NFKBIAABL1    NTRK1ABL1    PAG1ABL1    PARK2ABL1    PCNAABL1    PIK3R1ABL1    PLCG1ABL1    PRKDCABL1    PSMA4ABL1    PSMA7ABL1    PTPN6ABL1    RAD51ABL1    RAD9AABL1    RB1ABL1    RFX1ABL1    RYBPABL1    SHC1ABL1    SHDABL1    SHEABL1    SORBS2ABL1    SPTA1ABL1    SPTAN1ABL1    SRCABL1    STK4ABL1    STUB1ABL1    TERF1ABL1    TOPBP1ABL1    TP53ABL1    TP73ABL1    TUBABL1    UBCABL1    VAV1ABL1    WRNIP1ABL1    YTHDC1ABL1    ZDHHC16ABL2    ABL1ABL2    CATABL2    PSMA7ABL2    SORBS2ABLIM1    BEGAINABLIM1    CALCOCO2ABLIM1    HOOK2ABLIM1    LDOC1ABLIM1    TRAF2ABLIM1    TSC22D4ABLIM1    USHBP1ABLIM1    VIMABLIM3    ACTC1ABTB1    DNTTIP1ABTB2    CUL3ABTB2    DNTTABTB2    EEF1A1ABTB2    RBX1ABTB2    UBCACACA    BRCA1ACACA    CHGBACADVL    ACADVLACAN    FBLN2ACAP1    IFFO1ACCN1    ACCN3ACCN1    Pick1ACCN2    PICK1ACCN3    DLG4ACCN3    GOPCACCN3    LIN7BACCN3    MAGI1ACCS    ACCSACCS    FBF1ACD    POT1ACD    TERF1ACD    TERF2ACD    TINF2ACD    XRCC6ACHE    COL1A1ACIN1    RNPS1ACIN1    SAP18ACO1    FBXL5ACO1    UBCACP1    EPHA2ACP1    FNBP1LACP1    MRPL20ACP1    SFMBT1ACP5    C2orf18ACP6    C2orf18ACP6    DHCR7ACP6    DHX36ACP6    ERHACP6    GNG7ACP6    ILKACP6    LIMS1ACP6    RGS10ACP6    RSU1ACPP    ACPPACSM3    EHMT2ACTA1    CCT4ACTA1    CCT5ACTA1    CFL1ACTA1    DHX9ACTA1    DMDACTA1    DNASE1ACTA1    ERD10ACTA1    GCACTA1    HDAC4ACTA1    HDAC8ACTA1    NRAPACTA1    PCYT1BACTA1    RPS6KB1ACTA1    TMSB4XACTA1    TMSB4YACTA1    TRIP6ACTA2    CCT4ACTA2    CCT5ACTA2    PCYT1BACTB    ACTBACTB    ACTG1ACTB    ACTR2ACTB    ACTR3ACTB    CCT2ACTB    CCT5ACTB    CFL1ACTB    CFL2ACTB    CTGFACTB    Cct3ACTB    Cct4ACTB    Cct5ACTB    Cct6aACTB    Cct7ACTB    Cct8ACTB    DHX9ACTB    DSTNACTB    ESR1ACTB    HMMRACTB    HNRNPUACTB    Hspa1ACTB    NCALDACTB    NCF1ACTB    NCF2ACTB    PCYT1BACTB    POLR2AACTB    Pcyt1aACTB    Pcyt1ACTB    RAC1ACTB    RAC2ACTB    SSH1ACTB    SSH2ACTB    TAF11ACTC1    PDCD6IPACTC1    SYNE2ACTG1    ACTG1ACTG1    CFL1ACTG1    CFL2ACTG1    DSTNACTG1    PFN2ACTG1    SH3GL2ACTG1    TMSB4XACTL6A    EWSR1ACTL6A    FLIIACTL6A    KAT2AACTL6A    KAT5ACTL6A    RUVBL1ACTL6A    TP53ACTL6A    TRRAPACTL6A    YY1ACTL6B    CTBP1ACTN1    ACTN1ACTN1    CDK5R2ACTN1    CTNNA1ACTN1    DAG1ACTN1    MAGEA11ACTN1    MYOTACTN1    MYOZ1ACTN1    PDLIM1ACTN1    PKN1ACTN1    PYGBACTN1    SSX2IPACTN1    TTNACTN1    TUBA1AACTN1    XRCC4ACTN1    ZYXACTN2    ACTN3ACTN2    ADAM12ACTN2    DLG1ACTN2    GRIN2BACTN2    KCNA5ACTN2    MYOZ1ACTN2    MYPNACTN2    PDLIM1ACTN2    TNNACTN2    Tuba1aACTN3    ACTN2ACTN4    CAMK2AACTN4    CAMK2BACTN4    ESR1ACTN4    INO80ACTN4    Lc7ACTN4    MEF2AACTN4    MYOZ1ACTN4    MYOZ2ACTN4    PDLIM1ACTN4    VDRACTR1A    NUMA1ACTR3    ACTR2ACTR3    ARPC1BACTR3    ARPC2ACTR3    ARPC3ACTR3    ARPC4ACTR3    CTTNACTR3B    ACTR2ACTR3B    ARPC1AACTR3B    ARPC1BACTR3B    ARPC2ACTR3B    ARPC3ACTR3B    ARPC3P1ACTR3B    ARPC4ACTR3B    ARPC5ACTR3B    ARPC5LACTR3B    CDK4ACTR3B    KIAA1967ACTR3B    TWF2ACTR5    ACTL6AACTR5    ACTR8ACTR5    INO80ACTR5    INO80BACTR5    INO80CACTR5    INO80DACTR5    INO80EACTR5    MCRS1ACTR5    NFRKBACTR5    RUVBL1ACTR5    RUVBL2ACTR5    TFPTACTR5    UCHL5ACTR5    YY1ACTR8    ACTL6AACTR8    ACTR5ACTR8    INO80ACTR8    INO80BACTR8    INO80CACTR8    INO80DACTR8    INO80EACTR8    MCRS1ACTR8    NFRKBACTR8    RUVBL1ACTR8    RUVBL2ACTR8    TFPTACTR8    UCHL5ACTR8    YY1ACVR1    Ap2b1ACVR1    BMPR2ACVR1    Cdk14ACVR1    Chn1ACVR1    FNTAACVR1    FanclACVR1    Fbxo3ACVR1    Fcho1ACVR1    Fgd6ACVR1    Fkbp4ACVR1    GDF5ACVR1    IGSF1ACVR1    IkbkACVR1    IlkapACVR1    JuACVR1    Naa20ACVR1    Nkiras1ACVR1    NrasACVR1    Nuak2ACVR1    PlekACVR1    Plekhb1ACVR1    Rab17ACVR1    Rab33ACVR1    Rab3ACVR1    Rab6ACVR1    Rap2aACVR1    Rasd2ACVR1    Rhebl1ACVR1    Rhobtb1ACVR1    RhodACVR1    RhojACVR1    Rps27aACVR1    Rras2ACVR1    SMAD1ACVR1    SMAD5ACVR1    SMURF1ACVR1    Sqstm1ACVR1    Stat1ACVR1    Stx8ACVR1    TSC22D1ACVR1    Tgf1ACVR1    Ube2e3ACVR1    Ube2r2ACVR1    Uhmk1ACVR1    Usp21ACVR1    Usp39ACVR1    Wdr61ACVR1B    ACVR1ACVR1B    ACVR2AACVR1B    FKBP1AACVR1B    IGSF1ACVR1B    NEDD4LACVR1B    SMAD2ACVR1B    SMAD3ACVR1B    SMAD7ACVR1B    SMURF1ACVR1B    TSC22D1ACVR1B    UBCACVR2A    BMP6ACVR2A    GDF5ACVR2A    IGSF1ACVR2A    INHAACVR2A    INHBAACVR2A    MAGI2ACVR2A    SYNJ2BPACVR2B    ACVR1BACVR2B    BMP6ACVR2B    GDF5ACVR2B    IGSF1ACVR2B    MSTNACVRL1    IGSF1ACVRL1    TGFB1ACVRL1    TSC22D1ACY1    ACY1ACY1    TTC1ADA    ADORA1ADA    ADORA2AADA    DRD1ADA    NR3C1ADAM10    GRB2ADAM10    LCKADAM10    MAD2L1ADAM11    STC2ADAM12    IGFBP3ADAM12    IGFBP5ADAM12    PIK3R1ADAM15    GRB2ADAM15    HCKADAM15    LCKADAM15    MAD2L1ADAM15    SH3GL2ADAM15    SNX9ADAM15    TRIP13ADAM17    DLG1ADAM17    MAD2L1ADAM17    MAPK1ADAM19    ABI2ADAM19    COPB1ADAM2    CRYABADAM2    DNM1ADAM22    DLG4ADAM22    LGI1ADAM9    MAD2L2ADAM9    PRKCDADAM9    SH3GL2ADAM9    SNX9ADAMTS1    VEGFAADAMTSL4    CATSPER1ADAMTSL4    DLK2ADAMTSL4    KRTAP4-12ADAMTSL4    NTN4ADAP1    ANP32AADAP1    CSNK1A1ADAP1    NCLADAP1    PIK3CAADAP1    PRKCIADAP1    PRKCZADAP1    PRKD1ADAP2    EEF1GADAR    XPO1ADARB1    PIN1ADARB1    WWP2ADCY2    ADCY5ADCY5    ADCY5ADCY5    Mycbp2ADCY5    RGS2ADCY6    CHRNA7ADCYAP1    CPAMD8ADCYAP1    SCTRADD1    CALM1ADD1    HDAC1ADD1    ID2ADD1    ID3ADD1    SIN3AADD1    SMARCA2ADD1    SMARCA4ADD1    SMARCC1ADD1    SPTAN1ADD1    SPTBADH5    ADH5ADH5    CHD3ADH7    ADH7ADI1    DBTADNP    ARID1AADNP    SMARCA4ADNP    SMARCC2ADORA1    DRD1ADORA1    GNAI2ADORA2A    ADORA2AADORA2A    Actn1ADORA2A    Actn2ADORA2A    Actn3ADORA2A    Actn4ADORA2A    DRD2ADRA1B    AP2M1ADRA2B    EIF2B1ADRA2C    EIF2B1ADRB1    ARRB1ADRB1    GIPC1ADRB2    ADRB2ADRB2    ADRBK1ADRB2    AKAP12ADRB2    ARRDC3ADRB2    A2ADRB2    CAV3ADRB2    CUL2ADRB2    EGLN3ADRB2    EIF2B1ADRB2    GRB2ADRB2    NEDD4ADRB2    OPRD1ADRB2    PPP3CAADRB2    SLC9A3R1ADRB2    SLC9A3R2ADRB2    SRCADRB2    TCEB1ADRB2    UBCADRB2    VHLADRB3    SRCADRBK1    FSHRADRBK1    GNA15ADRBK1    GNAQADRBK1    HDAC6ADRBK1    PDCADRBK1    PDCLADRBK1    PDE6GADRBK1    PRKCBADRBK1    RHOADRBK1    SNCAADRBK1    SNCBADRBK1    SNCGADRBK1    SRCADRBK2    CXCR4ADRBK2    UBCADRM1    ATP6V0D2ADRM1    PSMC5ADRM1    PSMD1ADRM1    PSMD2ADRM1    PSMD4ADRM1    UBCADRM1    UCHL5AEBP2    RALYLAEBP2    SUZ12AES    AESAES    ARAES    GTF2E1AES    HMGB1AES    HNF1AAES    HNRNPABAES    MED31AES    PTRH2AES    RELAAES    SH3GL3AES    TLE1AES    TLE3AFAP1    ACTC1AFAP1    AFAP1AFAP1    PRKCAAFAP1    PRKCBAFAP1    PRKCDAFAP1    PRKCEAFAP1    PRKCGAFF1    AFF1AFF1    AFF4AFF1    BRD4AFF1    CCNT1AFF1    CDK9AFF1    DDX6AFF1    DOT1LAFF1    HEXIM1AFF1    HIST3H3AFF1    MLLAFF1    MLLT1AFF1    MLLT10AFF1    MLLT3AFF1    NPM1AFF1    NT5EAFF1    PCSK1AFF1    POLR2AAFF1    RELAAFF4    AFF1AFF4    CCNT1AFF4    CDK9AFF4    ELL2AFF4    MLLAFF4    MLLT1AFF4    MLLT3AFP    CCR5AGA    AGAAGAP2    EPB41L1AGAP2    PIK3R1AGFG1    EPS15AGFG2    EPS15AGL    UBCAGPS    GNPATAGR2    BRD7AGR2    CCDC90BAGR2    CRMP1AGR2    DAG1AGR2    LYPD3AGR2    MED31AGR3    DAG1AGR3    LYPD3AGRP    MC4RAGT    EWSR1AGTR1    ADRBK1AGTR1    AGTRAPAGTR1    ARRB2AGTR1    BDKRB2AGTR1    GRK5AGTR1    MAPK1AGTR1    TRAF3AGTR1    ZBTB16AGTR2    AGTRAPAGTR2    MTUS1AGTRAP    AGTRAPAGTRAP    GNB2L1AGXT2L2    AGXT2L2AHR    AIPAHR    ARNTAHR    CCNT1AHR    CTNNB1AHR    ESR1AHR    FOXA1AHR    GTF2F1AHR    GTF2F2AHR    HSP90AA1AHR    NCOA2AHR    NEDD8AHR    NR2F1AHR    NRIP1AHR    RB1AHR    RELAAHR    SMARCA4AHR    SRCAHR    TBPAHRR    ANKRA2AHRR    ESR1AHRR    HDAC4AHRR    HDAC5AHSP    ZC3H12AAI837181    AHNAKAI837181    ANXA5AI837181    ARF1AI837181    ARF3AI837181    ASS1AI837181    C11orf68AI837181    CALRAI837181    CANXAI837181    CAPRIN1AI837181    CDK1AI837181    CSDE1AI837181    DDX39AAI837181    DDX39BAI837181    DDX5AI837181    DHX15AI837181    EIF4A1AI837181    EIF4A3AI837181    EIF4HAI837181    FASNAI837181    GNB2L1AI837181    GOT2AI837181    GPIAI837181    HNRNPA3AI837181    HNRNPABAI837181    HNRNPKAI837181    HNRNPRAI837181    HNRNPUAI837181    NACAAI837181    NONOAI837181    P4HBAI837181    PA2G4AI837181    PABPC1AI837181    PDIA3AI837181    PDIA4AI837181    PDIA6AI837181    PFN1AI837181    PGK1AI837181    PHBAI837181    PHB2AI837181    PHGDHAI837181    PKM2AI837181    PPIAAI837181    PPIBAI837181    RANAI837181    RBMXAI837181    RCN1AI837181    RUVBL2AI837181    SERBP1AI837181    SETAI837181    SFPQAI837181    SRSF1AI837181    SRSF5AI837181    SRSF6AI837181    STRAPAI837181    SYNCRIPAI837181    TAGLN2AI837181    TFRCAI837181    TKTAI837181    TRAP1AI837181    UBA1AI837181    VCPAI837181    VDAC1AI837181    XRCC6AICDA    CTNNBL1AICDA    KPNA1AICDA    PRKDCAICDA    TUBB4BAIF1    CASP10AIF1    CASP8AIFM1    HSPA1AAIFM1    SETDB1AIFM1    STC2AIFM1    UBCAIFM1    XIAPAIMP1    PSMA7AIMP1    RARSAIMP1    SMURF2AIMP2    ACTBAIMP2    AIMP2AIMP2    C19orf57AIMP2    CEP170P1AIMP2    CHD3AIMP2    CNOAIMP2    DARSAIMP2    DARS2AIMP2    DEAF1AIMP2    DSN1AIMP2    FGBAIMP2    HSPA4AIMP2    IARSAIMP2    KARSAIMP2    KDRAIMP2    KIAA0947AIMP2    KIAA1377AIMP2    KLC2AIMP2    LMO3AIMP2    LNX1AIMP2    LUC7L2AIMP2    MATR3AIMP2    MCF2LAIMP2    PARK2AIMP2    PPP2R1AAIMP2    PSME1AIMP2    QARSAIMP2    RARSAIMP2    STUB1AIMP2    TP53AIMP2    TRMT2AAIMP2    UBCAIMP2    ZC3H12AAIP    AHRAIP    GNA13AIP    HSP90AA1AIP    STIP1AIPL1    NUB1AIRE    AIREAIRE    CHD6AIRE    DDX17AIRE    DDX5AIRE    EFTUD2AIRE    GEMIN5AIRE    HIST1H2ACAIRE    HIST1H2BOAIRE    HIST1H3AAIRE    HIST2H2BEAIRE    HSPA4AIRE    HSPA5AIRE    IPO7AIRE    KPNB1AIRE    LMNB1AIRE    MCM2AIRE    MCM5AIRE    MCM6AIRE    MSH2AIRE    MSH6AIRE    MYBBP1AAIRE    NASPAIRE    NOP56AIRE    NUP93AIRE    PABPC1AIRE    PARP1AIRE    PCNAAIRE    POLR2AAIRE    POLR2BAIRE    PRKDCAIRE    RAD21AIRE    RANBP2AIRE    RANBP9AIRE    RUVBL2AIRE    SMC1AAIRE    SMC3AIRE    SNRPBAIRE    SNRPD3AIRE    SRSF1AIRE    SRSF2AIRE    SRSF3AIRE    SSRP1AIRE    TOP2AAIRE    TRIM28AIRE    XPO1AIRE    XPOTAJAP1    CDH1AJAP1    CTNNB1AJUBA    PRMT5AJUBA    RARAAJUBA    RARGAJUBA    RXRGAJUBA    SLC1A2AJUBA    SNAI1AK1    MLL3AK4    KEAP1AKAP1    AMY1AAKAP1    C3orf15AKAP1    MYCBPAKAP1    PRKAR1AAKAP1    PRKAR1BAKAP1    PRKAR2AAKAP11    GSK3BAKAP11    PPP1CAAKAP11    PPP1CBAKAP11    PPP1CCAKAP11    PRKAR1AAKAP11    PRKAR2AAKAP11    PRKAR2BAKAP12    HDAC7AKAP12    PRKAR2AAKAP12    PRKCAAKAP13    ESR1AKAP13    GNA12AKAP13    GNAQAKAP13    PPARAAKAP13    RHOAAKAP13    RXRBAKAP13    THRAAKAP14    PRKAR2AAKAP17A    CCDC85BAKAP17A    NINLAKAP2    PRKAR2AAKAP3    AKAP4AKAP3    PRKAR2AAKAP3    ROPN1AKAP3    ROPN1LAKAP3    SPA17AKAP4    AKAP3AKAP4    FSIP1AKAP4    FSIP2AKAP4    PRKAR1AAKAP4    PRKAR2AAKAP5    CALM1AKAP5    Dlg1AKAP5    Dlg4AKAP5    Gria1AKAP5    Grin2AKAP5    PPP3CAAKAP5    PRKAR2BAKAP5    PRKCAAKAP6    PDE4AAKAP8    AMY1AAKAP8    CCND1AKAP8    CCND2AKAP8    CCND3AKAP8    DDX5AKAP8    MCM2AKAP8    PRKAR2AAKAP8L    CDC6AKAP8L    EMDAKAP8L    LBRAKAP8L    RNF43AKAP8L    TMPOAKAP8L    UBCAKAP9    CALM1AKAP9    CALM2AKAP9    CCNE1AKAP9    CSNK1DAKAP9    CSNK1EAKAP9    FNBP1AKAP9    PKN1AKAP9    PRKAR2AAKAP9    TRIP10AKAP9    TUBGCP3AKIP1    NEDD8AKIP1    PRKACAAKIP1    RELAAKIP1    SENP8AKIP1    SIRT1AKIRIN2    LNX1AKR1A1    EXOSC4AKR1B10    ACACAAKR1C2    AKR1C2AKR1C3    LRIF1AKR1C3    UBE2WAKR1C3    ZHX1AKR7A2    AKR7A3AKR7A3    AKR7A3AKT1    ACTA1AKT1    AKTIPAKT1    APOHAKT1    ARAKT1    ARFIP2AKT1    ARHGAP29AKT1    ARRB2AKT1    ASXL1AKT1    Akt2AKT1    BADAKT1    BPGMAKT1    BRAFAKT1    BRCA1AKT1    CARHSP1AKT1    CDC37AKT1    CDKN1BAKT1    CHEK1AKT1    CHN2AKT1    CHUKAKT1    COMMD1AKT1    CREBBPAKT1    DCTN1AKT1    DNAJB1AKT1    DNMT1AKT1    EEF1GAKT1    EP300AKT1    ERBB3AKT1    ESR1AKT1    EZH2AKT1    FANCAAKT1    FOXO1AKT1    GAB2AKT1    GSK3AAKT1    GSK3BAKT1    HSP90AA1AKT1    HSP90AB1AKT1    HSPA4AKT1    HSPB1AKT1    IKBKBAKT1    ILKAKT1    IMPDH2AKT1    IRAK1AKT1    KRT10AKT1    KTN1AKT1    MAP2K4AKT1    MAP3K8AKT1    MAPK14AKT1    MAPK8IP1AKT1    MAPKAPK2AKT1    MARK2AKT1    MDM2AKT1    MTCP1AKT1    MTORAKT1    MXD1AKT1    NCOA4AKT1    NCOR2AKT1    NF2AKT1    NOTCH1AKT1    NPM1AKT1    NR4A1AKT1    PA2G4AKT1    PAK1AKT1    PAK6AKT1    PDPK1AKT1    PI4K2BAKT1    PIAS1AKT1    PIAS2AKT1    PKN2AKT1    PPA1AKT1    PPLAKT1    PPP2CAAKT1    RAF1AKT1    SETDB1AKT1    SKP2AKT1    SMARCB1AKT1    SMARCC1AKT1    SMARCC2AKT1    STUB1AKT1    TCL1AAKT1    TCL1BAKT1    TERTAKT1    TRIB3AKT1    TRIM13AKT1    TSC1AKT1    TSC2AKT1    TTC3AKT1    UBCAKT1    XIAPAKT1    YWHAZAKT1    ZHX1AKT2    APPL1AKT2    CHEK1AKT2    CHUKAKT2    ESR1AKT2    MTCP1AKT2    SETDB1AKT2    SH3RF1AKT2    TCL1AAKT2    TCL1BAKT2    TTC3AKT2    XIAPAKT3    PRKCZAKT3    TTC3AKTIP    AKT1AKTIP    ASS1AKTIP    C10orf2AKTIP    DCTN1AKTIP    DZIP3AKTIP    EXOC7AKTIP    GTF3C1AKTIP    HDLBPAKTIP    HOOK1AKTIP    IARSAKTIP    IMMTAKTIP    KIAA1377AKTIP    MARCH5AKTIP    PDS5AAKTIP    POLA2AKTIP    RPA1AKTIP    TIMM50AKTIP    TRIM23AKTIP    TRIM41AKTIP    UTP14AALAS2    SUCLA2ALB    FCGRTALB    LUC7L2ALCAM    CD6ALDH1A1    ALDH1A1ALDH2    C14orf1ALDH2    C2orf18ALDH2    CRMP1ALDH2    HSPD1ALDH2    HSPE1ALDH2    IGSF21ALDH2    UNC119ALG10B    KCNH2ALG2    ALG2ALG2    ANXA11ALG2    ANXA7ALG2    HSP90AA1ALG2    LAMP1ALG2    PDCD6IPALG2    SEC31AALG2    TSG101ALG2    VPS28ALG2    VPS37AALK    CDK13ALK    CENPFALK    DYT10ALK    EIF4BALK    EPHA1ALK    EPHB2ALK    GAKALK    GRB2ALK    HSPD1ALK    IRF7ALK    IRS4ALK    JAK2ALK    JAK3ALK    KRT18ALK    KRT74ALK    MAP2K7ALK    MAP3K1ALK    MAP3K4ALK    MAP3K5ALK    MAPK1ALK    MAPK8IP3ALK    MEP1BALK    MTIF2ALK    MYBPC3ALK    MYLKALK    PDX1ALK    PIK3CBALK    PLCB2ALK    PLCG1ALK    PTNALK    RAB35ALK    RAD17ALK    SHC1ALK    SHC3ALK    SMC6ALK    SOCS1ALK    SOCS5ALK    STAT3ALK    UBASH3AALK    ZC3HC1ALKBH1    DNAJB6ALL1    CHD3ALL1    HDAC1ALL1    HDAC2ALL1    HIST1H3AALL1    MBD3ALL1    RANALL1    RBBP4ALL1    RBBP7ALL1    SAP30ALL1    SIN3AALL1    SMARCA2ALL1    SMARCB1ALL1    SMARCC1ALL1    SMARCC2ALL1    TAF1ALL1    TAF6ALL1    TAF9ALL1    TBPALOX12    ITGB4ALOX12    KRT5ALOX12    LMNAALOX12    TRIB1ALOX5    COTL1ALOX5    COTL1P1ALOX5    TGFBRAP1ALPI    AP3B1ALPI    IRF5ALS2CL    RAB5AALX1    IPO13ALX4    ALX4AMBP    A2MAMBP    ALBAMBP    AMBPAMBP    CD79AAMBP    FN1AMBRA1    ATG3AMBRA1    ATG4BAMBRA1    CUL4AAMBRA1    CUL4BAMBRA1    DDA1AMBRA1    DDB1AMBRA1    MAP1BAMBRA1    PARK2AMD1    AMD1AMFR    AIFM1AMFR    AMFRAMFR    ATP2A2AMFR    ATXN3AMFR    CANXAMFR    CCDC47AMFR    CD3DAMFR    CRMP1AMFR    CSE1LAMFR    CYP2E1AMFR    CYP3A4AMFR    DERL1AMFR    DERL2AMFR    DERL3AMFR    EEF1A1AMFR    ERLIN1AMFR    ERLIN2AMFR    FAF2AMFR    HAX1AMFR    HERPUD1AMFR    HMGCRAMFR    HSP90B1AMFR    HSPA4AMFR    HSPA5AMFR    HSPD1AMFR    HTTAMFR    INSIG1AMFR    KPNB1AMFR    PDIA2AMFR    RHOT1AMFR    RNF5AMFR    RPL5AMFR    SEC61BAMFR    SOD1AMFR    SRPRBAMFR    SYVN1AMFR    TCP1AMFR    TIMM50AMFR    TMUB1AMFR    TOM1L1AMFR    TRIM28AMFR    UBCAMFR    UBE2G2AMFR    UFD1LAMFR    Ube2g2AMFR    VCPAMIGO1    AMIGO1AMIGO1    AMIGO2AMIGO1    AMIGO3AMIGO2    AMIGO1AMIGO2    AMIGO2AMIGO2    AMIGO3AMIGO3    AMIGO1AMIGO3    AMIGO2AMIGO3    AMIGO3AMOT    AMOTL1AMOT    BAG3AMOT    DLG1AMOT    DYNLL1AMOT    DYNLL2AMOT    FOXK1AMOT    FOXK2AMOT    ITCHAMOT    LIN7AAMOT    LIN7CAMOT    LONP2AMOT    MPDZAMOT    MPP5AMOT    MPP7AMOT    NEDD4AMOT    NEDD4LAMOT    NF2AMOT    NINAMOT    SCLT1AMOT    UIMC1AMOT    USP11AMOT    YAP1AMOTL2    AMOTL2AMOTL2    GCC1AMOTL2    KRT20AMOTL2    MAGOHBAMPH    AP2B1AMPH    BIN1AMPH    CABIN1AMPH    CDK5R1AMPH    CLTCAMPH    DNM1AMPH    FBP1AMPH    ITSN1AMPH    JUNAMPH    PLD1AMPH    PLD2AMPH    REPS1AMPH    REPS2AMPH    SGIP1AMPH    SH3GL2AMPH    SYNJ1AMPH    SYNMAMPH    TP73AMPH    TXNL4BAMPH    VTNAMPH    XRCC4AMY1A    AKAP8ANAPC1    ANAPC11ANAPC1    ANAPC2ANAPC1    ANAPC4ANAPC1    ANAPC5ANAPC1    ANAPC7ANAPC1    CCNB1ANAPC1    CDC16ANAPC1    CDC23ANAPC1    CDC27ANAPC1    FZR1ANAPC1    PTTG1ANAPC10    CCNB1ANAPC10    PTTG1ANAPC10    SMAD2ANAPC10    SMAD3ANAPC11    ANAPC10ANAPC11    ANAPC2ANAPC11    CCNB1ANAPC11    CUL5ANAPC11    PTTG1ANAPC11    UBCANAPC11    UBE2L1ANAPC13    CCNB1ANAPC13    PTTG1ANAPC16    CCNB1ANAPC16    PTTG1ANAPC2    ANAPC11ANAPC2    ANAPC4ANAPC2    ANAPC5ANAPC2    BUB1BANAPC2    CCNB1ANAPC2    CDC20ANAPC2    CREBBPANAPC2    EP300ANAPC2    EPHA4ANAPC2    GRIA1ANAPC2    MAD2L1ANAPC2    PTTG1ANAPC2    UBE2CANAPC4    ANAPC1ANAPC4    ANAPC10ANAPC4    ANAPC11ANAPC4    ANAPC5ANAPC4    ANAPC7ANAPC4    APC2ANAPC4    BUB1BANAPC4    BUB3ANAPC4    C11orf51ANAPC4    CCNB1ANAPC4    CDC16ANAPC4    CDC20ANAPC4    CDC23ANAPC4    CDC27ANAPC4    FZR1ANAPC4    MAD2L1ANAPC4    PTTG1ANAPC5    ANAPC7ANAPC5    CCNB1ANAPC5    CDC27ANAPC5    FZR1ANAPC5    PABPC1ANAPC5    PTTG1ANAPC5    ZBTB16ANAPC7    CCNB1ANAPC7    CDC20ANAPC7    CREBBPANAPC7    EP300ANAPC7    FZR1ANAPC7    PTTG1ANGPTL4    ACTBANGPTL7    ANGPTL7ANK1    OBSCNANK1    RHAGANK1    TIAM1ANK1    TTNANK3    KCNC1ANK3    SPTBN4ANK3    TIAM1ANKRA2    ABL1ANKRA2    HDAC3ANKRA2    HDAC4ANKRA2    HDAC5ANKRA2    LRP2ANKRA2    MPLANKRA2    PDE3BANKRA2    RFX5ANKRD1    MYPNANKRD1    TTNANKRD11    ANKRD11ANKRD11    HDAC3ANKRD11    NCOA2ANKRD11    NCOA3ANKRD12    HDAC3ANKRD12    TADA3ANKRD13B    RPLP1ANKRD2    HBP1ANKRD2    TCAPANKRD2    YBX1ANKRD2    ZBTB3ANKRD23    MYPNANKRD23    TTNANKRD24    EEF1A1ANKRD24    LRIF1ANKRD24    UNC119ANKRD32    RAD18ANKRD55    ZSCAN1ANKRD6    AXIN2ANKRD6    CSNK1EANKRD6    GSK3BANKS1A    EPHA8ANKS1B    UBCANKZF1    VCPANP32A    HIST1H3AANP32A    MAP1BANP32A    SETANP32A    TAF1AANP32A    XPO1ANTXR2    UBCANXA1    ANXA1ANXA1    ANXA5ANXA1    APBB1ANXA1    C14orf1ANXA1    C1orf123ANXA1    CCT7ANXA1    COPS6ANXA1    CSADANXA1    FAF1ANXA1    GAPDHANXA1    KLHL23ANXA1    KRT8ANXA1    LRIF1ANXA1    MLL4ANXA1    OTUB1ANXA1    RPA1ANXA1    S100A11ANXA1    SUMO1ANXA1    UBCANXA1    UBE2D1ANXA1    UBE3AANXA1    UNC119ANXA1    XRCC6ANXA11    ALG2ANXA11    PDCD6ANXA11    PLSCR1ANXA11    S100A6ANXA2    APOHANXA2    CTSBANXA2    PLATANXA2    S100A10ANXA2    STAT6ANXA2    gagANXA3    IGSF21ANXA3    TP53ANXA3    UBR1ANXA3    UNC119ANXA4    NFKB1ANXA4    NMT2ANXA4    SMPD1ANXA5    EEDANXA5    FDFT1ANXA5    ITGB5ANXA6    CDC73ANXA6    Rasa1ANXA6    S100A1ANXA6    S100BANXA7    A1BGANXA7    A2MANXA7    ACTBANXA7    ACTL6BANXA7    ADAMTS10ANXA7    ALG2ANXA7    ANGPT2ANXA7    APLP1ANXA7    ATP5BANXA7    ATP6V1AANXA7    ATXN3ANXA7    BAG6ANXA7    C14orf1ANXA7    CCDC90BANXA7    CCT7ANXA7    CDK4ANXA7    CELF3ANXA7    CENPBANXA7    CHGBANXA7    CLEC3BANXA7    COL11A2ANXA7    COL4A2ANXA7    COL4A5ANXA7    COPS6ANXA7    CPNE2ANXA7    CPNE6ANXA7    CPSF3LANXA7    CRMP1ANXA7    CSADANXA7    CTSBANXA7    DDAH2ANXA7    DMPKANXA7    DOCK7ANXA7    DVL1ANXA7    DYNC1I1ANXA7    EEF1A1ANXA7    EXT2ANXA7    F13A1ANXA7    FAF1ANXA7    FBN3ANXA7    FGBANXA7    FLAD1ANXA7    GAPDHANXA7    GBP2ANXA7    GDF9ANXA7    GNB2ANXA7    GNB5ANXA7    HADHBANXA7    HMGXB3ANXA7    HOXD8ANXA7    INPP5KANXA7    KLHL23ANXA7    LRIF1ANXA7    MED31ANXA7    MLL4ANXA7    MPPED1ANXA7    MSH2ANXA7    NGFRANXA7    NMT2ANXA7    NPRL2ANXA7    OTUB1ANXA7    PAAF1ANXA7    PDHBANXA7    PKM2ANXA7    PLD3ANXA7    PSMB10ANXA7    QARSANXA7    RBBP4ANXA7    RBM48ANXA7    RPA1ANXA7    RPL13ANXA7    RPS2ANXA7    SDF4ANXA7    SEMA5BANXA7    SETDB1ANXA7    SMPD1ANXA7    SP110ANXA7    SRIANXA7    SUMO3ANXA7    TAF5LANXA7    TIAM2ANXA7    TLE1ANXA7    TMEM108ANXA7    TMSB4XANXA7    TP53ANXA7    TRMT2AANXA7    TUBA1AANXA7    TUBB2BANXA7    TUBB3ANXA7    UBE2D1ANXA7    UNC119ANXA7    USP4ANXA7    VIMANXA7    WDR18ANXA7    WDR73ANXA7    ZBTB16ANXA7    ZNF135ANXA7    ZNF431ANXA9    NEDD4ANXA9    UBCAP1B1    AMPHAP1B1    AP1G1AP1B1    AP1M1AP1B1    AP2M1AP1B1    ARF1AP1B1    KIF13AAP1G1    AP1B1AP1G1    AP1M1AP1G1    AP1M2AP1G1    AP1S1AP1G1    AP2M1AP1G1    AP2S1AP1G1    ARF1AP1G1    CLTCAP1G1    JUNAP1G1    NECAP1AP1G1    NECAP2AP1G1    RABEP1AP1G1    SYNRGAP1G1    SYPAP1G1    gagAP1G2    NEDD4AP1G2    SYNRGAP1M1    FXR2AP1M1    LDOC1AP1M1    RUNDC3AAP1M1    TIFAAP1M1    ZBTB8AAP1M2    EHD2AP1M2    SCNN1AAP1M2    SCNN1BAP1M2    SCNN1GAP1S1    AP1G1AP1S1    AP1G2AP1S1    ARMC6AP1S1    EBLN2AP1S1    RAB10AP1S1    SEC61A1AP1S1    SLC16A1AP1S2    AP1G1AP1S2    AP1G2AP2A1    RAB11FIP2AP2A2    AMPHAP2A2    DAB2AP2B1    AP1M1AP2B1    AP1M2AP2B1    AP2M1AP2B1    ARRB2AP2B1    ATP6V1G1AP2B1    BUB1BAP2B1    DHX58AP2B1    FAM46CAP2B1    KIAA0408AP2B1    LDLRAP1AP2B1    MEA1AP2B1    MLH1AP2B1    NECAP2AP2B1    NUP54AP2B1    POM121AP2B1    RIBC2AP2B1    TERF2IPAP2B1    THAP1AP2B1    TUBGCP4AP2M1    ADRA1BAP2M1    AQP4AP2M1    CD22AP2M1    CLEC4MAP2M1    CTLA4AP2M1    DPPA2AP2M1    DVL2AP2M1    EHD2AP2M1    FXR2AP2M1    IKZF1AP2M1    MED4AP2M1    RTDR1AP2M1    RUNDC3AAP2M1    TBC1D5AP2M1    UBCAP2M1    ZBTB8AAP2S1    KHKAP2S1    POLQAP3B1    ARF5AP3B1    ARF6AP3S1    IRS1AP3S2    AP3B1AP3S2    AP3D1AP3S2    AP3M1AP3S2    ARF1AP3S2    ARF6AP4B1    AP4E1AP4B1    AP4M1AP4E1    AP4B1AP4E1    AP4S1AP4M1    AP4B1AP4M1    AP4E1APAF1    APIPAPAF1    BCL2L1APAF1    CASP4APAF1    CASP8APAF1    CASP9APAF1    HSP90AA1APAF1    HSPA4APAF1    NLRP1APBA1    APPAPBA1    CASKAPBA1    CCSAPBA2    APPAPBA2    CLSTN1APBA2    NECAB3APBA2    RELAAPBB1    ABI1APBB1    APBB1APBB1    APLP1APBB1    APLP2APBB1    APPAPBB1    CCDC97APBB1    CHERPAPBB1    CPSF6APBB1    CPSF7APBB1    CYFIP1APBB1    CYFIP2APBB1    DDX17APBB1    DDX3XAPBB1    DDX46APBB1    DHX15APBB1    DHX9APBB1    DIAPH1APBB1    DIAPH2APBB1    ENAHAPBB1    EVLAPBB1    HDAC1APBB1    HNRNPH1APBB1    HNRNPKAPBB1    HTATSF1APBB1    KAT5APBB1    KHDRBS1APBB1    KHSRPAPBB1    LRP1APBB1    NEDD4LAPBB1    NEDD8APBB1    NONOAPBB1    Nedd4lAPBB1    PABPC1APBB1    PQBP1APBB1    PTBP1APBB1    RBM17APBB1    RPL4APBB1    SETAPBB1    SF1APBB1    SF3A1APBB1    SF3A2APBB1    SF3A3APBB1    SF3B1APBB1    SF3B2APBB1    SF3B3APBB1    SF3B4APBB1    SFPQAPBB1    TFCP2APBB1    THRAP3APBB1    TSHZ3APBB1    U2AF2APBB1    VASPAPBB1    WASAPBB1    WASF2APBB1    WASLAPBB1    WBP11APBB1    WIPF1APBB1    WIPF2APBB1    YBX1APBB1    YLPM1APBB1    YWHAGAPBB2    APPAPBB3    APLP1APBB3    APLP2APBB3    APPAPC    ACTN1APC    AGFG1APC    ANKRD17APC    ANXA7APC    AP2B1APC    APCAPC    AXIN1APC    C4AAPC    CGNL1APC    COG4APC    COG5APC    CREBBPAPC    CSNK2A1APC    CSNK2BAPC    CTBP1APC    CTNNA1APC    CTNNB1APC    CYTH2APC    DLG3APC    DLGAP1APC    DSTAPC    EPAS1APC    ERBB2IPAPC    EXPH5APC    FAM214AAPC    FBXO30APC    FHOD1APC    FLNAAPC    GIGYF2APC    GOLGA2APC    HGSAPC    HNRNPMAPC    HSPA5APC    ING5APC    JUPAPC    KIAA1328APC    KIF5BAPC    KIFAP3APC    KRT13APC    KRT14APC    KRT15APC    KRT17APC    KRT19APC    KRT23APC    KRT5APC    LAMA3APC    LAMA4APC    LPHN1APC    MACF1APC    MAPRE1APC    MAPRE2APC    MBD5APC    MCM3APAPC    MUC1APC    MYH10APC    MYH11APC    MYO6APC    NAV1APC    NAV2APC    NAV3APC    NCKAP5APC    NCKAP5LAPC    ND4APC    NEBAPC    NOSTRINAPC    NUP153APC    NUP214APC    NUP54APC    NUP98APC    NUPL1APC    NUPL2APC    PNISRAPC    POM121APC    POM121CAPC    PPP1R13BAPC    PPP2R5AAPC    PSMD1APC    PSMD4APC    RANBP2APC    RANBP9APC    RBM4BAPC    RPS27APC    SEC31AAPC    SETDB1APC    SIAH1APC    SMC3APC    SNRNP200APC    SPECC1LAPC    SPTBN1APC    SPTBN2APC    SYNE1APC    TAF1APC    TFAP2AAPC    TPRAPC    TRIM21APC    TUBA4AAPC    UBCAPC    XPO1APC    ZFP106APC    ZRANB1APC11    UBE2D2APC2    ACTA1APC2    ANAPC1APC2    ANAPC10APC2    ANAPC11APC2    ANAPC4APC2    ANAPC5APC2    ANAPC7APC2    APC2APC2    CDC16APC2    CDC23APC2    CDC26APC2    CDC27APC2    CDH1APC2    CTNNB1APC2    UBCAPCS    APCSAPCS    FCGR1AAPCS    FCGR3AAPCS    FCGR3BAPCS    GOT2APCS    HES1APEH    APEHAPEH    IST1APEH    UBA5APEX1    ANP32AAPEX1    HIF1AAPEX1    HOXC13APEX1    MDM2APEX1    POLR3DAPEX1    SETAPEX1    TCF21APEX1    XRCC1APEX1    XRCC5APEX2    EFEMP2APEX2    HOOK2APEX2    PCNAAPH1A    NCSTNAPH1A    PSEN1APH1A    PSEN2APH1A    PSENENAPIP    APAF1APIP    APIPAPIP    LNX1APIP    NUDT18APIP    VPS25APITD1    APITD1APITD1    BLMAPITD1    C17orf70APITD1    C19orf40APITD1    FANCAAPITD1    FANCBAPITD1    FANCFAPITD1    FANCGAPITD1    FANCLAPITD1    FANCMAPITD1    RMI1APITD1    RMI2APITD1    STRA13APITD1    TOP3AAPLF    PARP1APLP1    DAB1

Abr Writing · Accepted Answer

Assignment_5.ipynb
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "tEdcbX_zFQ3y"
   },
   "source": [
    "Importing the necessary libraries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "colab": {},
    "colab_type": "code",
    "id": "CjUaJqSfFQ34"
   },
   "outputs": [],
   "source": [
    "import pandas as pd
",
    "import numpy as np
",
    "import matplotlib.pyplot as plt
",
    "import collections
",
    "import itertools
",
    "from scipy.stats import mannwhitneyu as wilcox
",
    "import networkx as nx"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "94c-lvvYFQ4k"
   },
   "source": [
    "# Part 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 202
    },
    "colab_type": "code",
    "id": "sv1tPvW-FQ4l",
    "outputId": "1b8d79cc-c94f-4c03-c0fd-e305d8b806a2"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "
",
       "
",
       "    .dataframe tbody tr th:only-of-type {
",
       "        vertical-align: middle;
",
       "    }
",
       "
",
       "    .dataframe tbody tr th {
",
       "        vertical-align: top;
",
       "    }
",
       "
",
       "    .dataframe thead th {
",
       "        text-align: right;
",
       "    }
",
       "
",
       "
",
       "  
",
       "    
",
       "      
",
       "      OFFICIAL_SYMBOL_A
",
       "      OFFICIAL_SYMBOL_B
",
       "    
",
       "  
",
       "  
",
       "    
",
       "      0
",
       "      1810055G02Rik
",
       "      MPRIP
",
       "    
",
       "    
",
       "      1
",
       "      1810055G02Rik
",
       "      RAI14
",
       "    
",
       "    
",
       "      2
",
       "      1810055G02Rik
",
       "      TPM1
",
       "    
",
       "    
",
       "      3
",
       "      2810046L04Rik
",
       "      ARF1
",
       "    
",
       "    
",
       "      4
",
       "      2810046L04Rik
",
       "      ARF3
",
       "    
",
       "  
",
       "
",
       ""
      ],
      "text/plain": [
       "  OFFICIAL_SYMBOL_A OFFICIAL_SYMBOL_B
",
       "0     1810055G02Rik             MPRIP
",
       "1     1810055G02Rik             RAI14
",
       "2     1810055G02Rik              TPM1
",
       "3     2810046L04Rik              ARF1
",
       "4     2810046L04Rik              ARF3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ppi = pd.read_csv('human ppi.txt', sep="\s+")
",
    "display(ppi.head())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "B5MfBy14FQ47"
   },
   "source": [
    "Adding nodes to the graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "colab": {},
    "colab_type": "code",
    "id": "NcdtiBPiFQ5B"
   },
   "outputs": [],
   "source": [
    "G=nx.Graph()
",
    "nodes = ppi.OFFICIAL_SYMBOL_A.append(ppi.OFFICIAL_SYMBOL_B).unique()
",
    "G.add_nodes_from(nodes)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "WlMoK2M7FQ5J"
   },
   "source": [
    "Adding edges to the graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "colab": {},
    "colab_type": "code",
    "id": "hTWR9eQNFQ5L"
   },
   "outputs": [],
   "source": [
    "G.add_edges_from(ppi.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "oDJZm-_hFQ5i"
   },
   "source": [
    "## Average Clustering Coefficient"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 35
    },
    "colab_type": "code",
    "id": "tZBhKlgPFQ5k",
    "outputId": "2ae49a57-8947-467a-f021-0106a119c786"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.20981150204746712"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(nx.average_clustering(G))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "lcYV5qYhFQ5u"
   },
   "source": [
    "## Scale Free Structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "yXM44PMVF-pV"
   },
   "source": [
    "Plotting the degree distribution"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 295
    },
    "colab_type": "code",
    "id": "djDnRUtCFQ5w",
    "outputId": "127a312e-b09e-42c3-d38d-892f43fc0b3b"
   },
   "outputs": [
    {
     "data": {
      "image/png":

Assignment 1 Assignment 5 • Write a script which can calculate the degree and clustering coefficient for every node (protein) in the human protein interaction network (attached). Now calculate the...

Solution