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Copy pathannotate-all.scm
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annotate-all.scm
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(load "load-files.scm")
; (start-cogserver "grid.conf")
; (start-cogserver "debug.conf")
(load "setup.scm")
(load "stats.scm")
(report-avg-gc-cpu-time)
(load-all)
(report-avg-gc-cpu-time)
(define gene-list (list
"TSPAN6"
"NDUFAF7"
"RBM5"
"SLC7A2"
"NDUFAB1"
"DVL2"
"SKAP2"
"DHX33"
"MSL3"
"BZRAP1"
"GTF2IRD1"
"IL32"
"RPS20"
"SCMH1"
"CLCN6"
"RNF14"
"ATP2C1"
"IGF1"
"GLRX2"
"FAS"
"ATP6V0A1"
"FBXO42"
"JADE2"
"PREX2"
"NOP16"
"LMO3"
"R3HDM1"
"ERCC8"
"HOMER3"
"USE1"
"OPN3"
"SZRD1"
"ATG5"
"CAMK2B"
"MPC1"
"MRPS24"
"ZNF275"
"TAF2"
"TAF11"
"IPO5"
"NDUFB4"
"DIP2B"
"MPPED2"
"IARS2"
"ERLEC1"
"UFD1L"
"PDCD2"
"ACADVL"
"ENO1"
"FRYL"
"SEC31B"
"KIFAP3"
"NT5C2"
"GPC4"
"ITGA8"
"PPP2R5C"
"RBFOX1"
"ITM2A"
"NRD1"
"VDAC3"
"CBFA2T2"
"FKBP7"
"SAR1A"
"DUSP13"
"PGR"
"EPB41L3"
"OXCT1"
"SLC27A5"
"WBP11"
"NCOA1"
"MAPRE3"
"MGST2"
"DIMT1"
"RBM22"
"TMED2"
"HUWE1"
"NLK"
"UIMC1"
"GNAS"
"COQ9"
"NSFL1C"
"TASP1"
"MRPS33"
"NDUFB2"
"TXNL1"
"MYL6"
"HDAC6"
"DHPS"
"CREM"
"PSMD8"
"CIRBP"
"HNRNPM"
"SF3A1"
"POLR2F"
"HMGXB4"
"CHKB"
"ZMAT5"
"RBM23"
"VTI1B"
"TIMM9"
"GSTZ1"
"RPS6KA5"
"PSMB5"
"PFDN4"
"PSMA7"
"NDUFAF5"
"ATP1B4"
"ALG13"
"SUV39H1"
"SCML2"
"PGK1"
"KLF5"
"TSC22D1"
"MGRN1"
"SLC7A6"
"CMC2"
"CPPED1"
"MYEF2"
"CPQ"
"LEPROTL1"
"PPP2CB"
"KLHDC4"
"POP4"
"AKT2"
"RABAC1"
"CARD8"
"PON2"
"SSBP1"
"BUD31"
"MEST"
"CHCHD3"
"COA1"
"BLVRA"
"PLGRKT"
"BAG1"
"EXOSC3"
"RASSF4"
"KAZALD1"
"PITRM1"
"EBF3"
"LGI1"
"MTMR4"
"CDK5RAP3"
"ENO3"
"ICAM2"
"EZH1"
"MRPL27"
"HDAC5"
"DUSP3"
"DCUN1D4"
"NDUFC1"
"ZBTB16"
"COMMD9"
"ATP5B"
"ELK3"
"ALDH2"
"STX2"
"GPR133"
"MRPL51"
"GAPDH"
"TPI1"
"TMEM14C"
"GCNT2"
"NCOA7"
"FANCE"
"E2F3"
"ACOT13"
"COX7A2"
"ENPP5"
"PCDHB2"
"TMCO6"
"TTC1"
"POLR3G"
"BNIP1"
"TIMMDC1"
"BCL6"
"FAM162A"
"PRKAR2A"
"TUSC2"
"SSR3"
"MOB1A"
"NCL"
"MPV17"
"HSPE1"
"ZNF142"
"ID2"
"PNO1"
"TMEM59"
"LAMTOR2"
"LEPR"
"CTH"
"TMEM9"
"MRPS15"
"SDHB"
"FAAH"
"DPH5"
"ANKRD13C"
"VAMP8"
"NDUFB3"
"GDA"
"MAPKAP1"
"YPEL5"
"RCL1"
"GRIA2"
"PCMT1"
"KIAA1217"
"PAIP2"
"ARL1"
"SOCS2"
"ECHDC2"
"A1BG"
"ZNF211"
"GTDC1"
"CCDC18"
"HNRNPA2B1"
"FAM126A"
"CLTA"
"CISD1"
"CDKN2C"
"RASSF8"
"ATP7B"
"ITIH5"
"SMUG1"
"NDUFAF4"
"PLA2G12A"
"PFKFB2"
"ATP5E"
"STAMBP"
"SNRNP27"
"NQO2"
"EMC3"
"TMTC4"
"SNRPD2"
"ID1"
"KDM5C"
"ST3GAL3"
"EMC1"
"UQCR11"
"RNF6"
"SHFM1"
"STEAP4"
"RBM48"
"TUBGCP6"
"EMC4"
"RABL5"
"MTX2"
"TXNDC17"
"DAD1"
"ECSIT"
"CDC16"
"RPL36"
"MRPL34"
"LSM4"
"CYP2E1"
"ZNF337"
"PRRC2B"
"COX4I1"
"NFATC1"
"PDLIM4"
"PSME3"
"NDUFA2"
"RAF1"
"ENOSF1"
"MRPL35"
"SERPINF1"
"GRSF1"
"WBP2"
"PRMT7"
"POMP"
"MYH8"
"BEX2"
"ACTR3B"
"ARL8B"
"EMC7"
"LAMTOR5"
"KCTD1"
"DDB2"
"PUM1"
"NREP"
"CTSL"
"FAM189A2"
"MDFIC"
"CAPRIN1"
"CD63"
"TSPAN31"
"MRPL44"
"NDUFB5"
"TANK"
"VPS45"
"PSMB7"
"UBAP2"
"GRHPR"
"BPHL"
"UQCC2"
"NUMA1"
"DCUN1D5"
"UNC13C"
"TUBGCP4"
"SLC28A2"
"CYP1B1"
"COX17"
"PARP16"
"HERC5"
"PPA2"
"LGR5"
"NEDD1"
"SLAIN1"
"GRTP1"
"TMX1"
"SERF2"
"SRP14"
"WDR61"
"TPM1"
"SEC11A"
"PMM2"
"MYLK3"
"CLTC"
"GAREM"
"GREB1L"
"RNF165"
"TXNL4A"
"NFIC"
"PSMB6"
"PSMA5"
"CELSR2"
"TIPRL"
"UFC1"
"SETDB1"
"ADAMTSL4"
"JTB"
"HAX1"
"ACP1"
"NVL"
"DEGS1"
"PSEN2"
"PDIA6"
"SFXN5"
"ZNF385B"
"UBR3"
"GULP1"
"ATG3"
"SRPRB"
"TMEM108"
"SLIT2"
"DDIT4L"
"PAM"
"TSLP"
"ATG12"
"BOD1"
"MYLK4"
"DYNLT1"
"PSPH"
"ATXN7L1"
"ZMYM3"
"ARHGAP36"
"HMBOX1"
"PXDNL"
"GOLGA7"
"POLR2K"
"EIF3H"
"NDUFB9"
"TATDN1"
"FAM171A1"
"FAM188A"
"GSTO1"
"EIF3M"
"ARFGAP2"
"DAK"
"CPSF7"
"CABLES2"
"SAP18"
"HNMT"
"TIMM8B"
"PTS"
"NDUFC2"
"BICD1"
"ZNF385D"
"GEMIN6"
"ATP5A1"
"CCDC50"
"UTRN"
"ZNF117"
"RASSF3"
"HNRNPU"
"TRIP12"
"LGI4"
"MSI2"
"UCHL1"
"ATP5G3"
"TCEB1"
"PSMA8"
"DPH3"
"ACSS1"
"TMEM55A"
"GOLGA7B"
"CNOT8"
"NUP205"
"KCNMA1"
"SCAF4"
"MALSU1"
"PDE6D"
"MUM1L1"
"AFAP1L1"
"WDR19"
"MRPL17"
"CNNM4"
"ZFAND2B"
"AGPAT6"
"SNF8"
"CBR1"
"TPPP3"
"CCDC28B"
"SSU72"
"PCNT"
"PCYT1A"
"COX7A1"
"BCL6B"
"POLR3K"
"NXF1"
"OLFML2B"
"MRPL55"
"RFTN2"
"VSNL1"
"RPRD2"
"BOLA3"
"MRPS18C"
"ARPC2"
"SUCLG1"
"PPM1L"
"ADAMTS9"
"ELP6"
"SMIM12"
"SFMBT1"
"RAD54L2"
"HPGD"
"ARFIP1"
"UQCRQ"
"HCN1"
"IQUB"
"SUN1"
"DCAF13"
"NDUFB6"
"CFL2"
"KLHDC2"
"TRUB1"
"ZFYVE1"
"PSMC3"
"DPCD"
"ALKBH3"
"CCT2"
"ZNF202"
"USP54"
"NDST2"
"SEC11C"
"CENPV"
"HSP90B1"
"AP1G1"
"PPIB"
"FAM96A"
"SMAD3"
"PDIA3"
"FBXO22"
"ATP5L"
"GPX4"
"ATP5H"
"POLR2G"
"COPS6"
"RAB4A"
"DNAJC7"
"COA6"
"MMADHC"
"MPLKIP"
"HEXIM2"
"COL3A1"
"CNNM3"
"USP39"
"RNF181"
"LRRC28"
"PPIC"
"STXBP6"
"MFF"
"ATP5I"
"PARM1"
"NSMCE1"
"EFNA1"
"CRADD"
"SIN3A"
"CNBP"
"ZNF32"
"TOR1AIP2"
"BRD3"
"SF3B5"
"STX8"
"UBB"
"DNAJC18"
"NUDCD2"
"GPR27"
"KBTBD2"
"TRIAP1"
"MTSS1"
"ZNF160"
"FEZ2"
"FAM86JP"
"RBKS"
"EXOSC1"
"PDE7B"
"MRPL36"
"BPTF"
"ZNF540"
"EXOSC10"
"FRMD3"
"TP53RK"
"SYNPO2"
"MYEOV2"
"MRPL52"
"TMEM134"
"BNC2"
"KDM2A"
"RHOD"
"COMMD1"
"GLRX"
"DMRT2"
"FAM86B3P"
"MINOS1"
"UQCRH"
"PHC3"
"USMG5"
"HOXB2"
"NRROS"
"MSRB3"
"SNAPC5"
"MRPL11"
"IL20RB"
"AKIRIN1"
"TMEM167A"
"NDUFA11"
"CADM2"
"LSM1"
"TMEM9B"
"SCUBE2"
"UCP3"
"PAAF1"
"MRPL48"
"RTTN"
"KCMF1"
"RMDN1"
"IRX5"
"MAMSTR"
"POLE"
"FAM210A"
"ATOX1"
"KIAA0195"
"MLF1"
"GRAMD1C"
"BOLA1"
"TMEM11"
"RIIAD1"
"SEPW1"
"MAGED1"
"FCER1A"
"PSMG4"
"SSR4"
"TRAPPC5"
"PLAG1"
"LSM10"
"COA4"
"NEUROG1"
"MRPS11"
"MRPS16"
"FAM104B"
"SATB1"
"NDN"
"CNOT10"
"ZNF662"
"CEP57L1"
"SFXN4"
"FAM162B"
"DENND5A"
"UBE2F"
"PCDH9"
"MROH7"
"NDUFA12"
"APOO"
"PTRHD1"
"RPS27L"
"ADSSL1"
"UBALD2"
"ROR1"
"NR2F2"
"PSMD13"
"ANKFY1"
"ZNF529"
"POLR1D"
"TOR3A"
"PPP1CC"
"RGS9BP"
"KRT10"
"GPATCH8"
"RPS19BP1"
"CMC1"
"MAGI2"
"EXD3"
"MORN2"
"COL4A5"
"COMMD6"
"S100A16"
"RNFT1"
"HN1"
"BLOC1S2"
"LCOR"
"XPNPEP3"
"ACN9"
"TECPR2"
"TOMM7"
"ADA"
"NOP9"
"CASP4"
"METTL9"
"ZNF398"
"ZNF682"
"MRPL21"
"HTT"
"COL4A6"
"PHF2"
"FAM118B"
"FAM49A"
"MRPL42"
"UBL5"
"CCDC69"
"NCOA6"
"MT-ND5"
"ZNF521"
"MT-ND3"
"SELT"
"OSTC"
"TSEN15"
"MT-ND4"
"DCLRE1A"
"CCDC167"
"DMD"
"SNORA63"
"TATDN3"
"FAM229B"
"INPP5B"
"COL15A1"
"ZBTB48"
"ZNF783"
"FLJ00104"
"SARNP"
"DNAJC19"
"SNORA12"
"U3"
"U3"
"SUPT4H1"
"ANKRD39"
"NDUFS3"
"SLC23A3"
"ARL16"
"ZSWIM7"
"COL28A1"
"SLC35E2"
"TENM3"
"FAM19A5"
"TPI1P1"
"OST4"
"EEF1DP3"
"HSBP1"
"MCTS1"
"DICER1-AS1"
"CDKN2AIPNL"
"FAM200B"
"GOLGA2P5"
"MRPL33"
"NME1-NME2"
"UBE2V1"
"SMIM20"
"APOPT1"
"CUX1"
"UBE2F-SCLY"
"GOLGA7B"
"NCBP2-AS2"))
(define (run-all)
(define start (current-time))
(format #t "Start annotation of ~A genes\n" (length gene-list))
(report-avg-gc-cpu-time)
(annotate-genes gene-list "agingSymbols"
"[{\"function_name\": \"gene-pathway-annotation\", \"filters\": [{\"filter\": \"pathway\", \"value\": \"smpdb reactome\"},{\"filter\": \"include_prot\", \"value\": \"True\"}, {\"filter\": \"include_sm\", \"value\": \"False\"},{\"filter\": \"coding\", \"value\": \"True\"},{\"filter\": \"noncoding\", \"value\": \"True\"}, {\"filter\": \"biogrid\", \"value\": \"0\"}]}, {\"function_name\": \"gene-go-annotation\", \"filters\": [{\"filter\": \"namespace\", \"value\": \"biological_process cellular_component molecular_function\"}, {\"filter\": \"parents\", \"value\": \"0\"}, {\"filter\": \"protein\", \"value\": \"True\"}]}, {\"function_name\": \"include-rna\", \"filters\": [{\"filter\": \"coding\", \"value\": \"True\"},{\"filter\": \"noncoding\", \"value\": \"True\"},{\"filter\": \"protein\", \"value\": \"1\"}]},{\"function_name\": \"biogrid-interaction-annotation\", \"filters\": [{\"filter\": \"interaction\", \"value\": \"Proteins\"}]}]")
(gc)
(report-avg-gc-cpu-time)
(format #t "\nRan annotation in ~A seconds\n" (- (current-time) start))
*unspecified*
)
(run-all)
; (report)