xuchuanyin / workbench

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2019年5月6日 lab8 #94

Open xuchuanyin opened 5 years ago

xuchuanyin commented 5 years ago

following is the kmeans_cluster.R

xuchuanyin commented 5 years ago

kmeans_cluster.R.txt

xuchuanyin commented 5 years ago

Part3.R.txt

xuchuanyin commented 5 years ago

Part3.R.txt

xuchuanyin commented 5 years ago

gene_desc_func <- gene_info[row.names(expr_data), c("description", "gene_function")] print(gene_desc_func)

xuchuanyin commented 5 years ago

Part3.R.txt

xuchuanyin commented 5 years ago

Part3.R.txt

xuchuanyin commented 5 years ago

top_go_analysis.r.txt

xuchuanyin commented 5 years ago

top_go_plot

xuchuanyin commented 5 years ago

ORF gene_name description YBR183W YBR183W UNKNOWN; SIMILAR TO H. INFLUENZAE LIC-1 YCL059C YCL059C KRR1 ESSENTIAL YCR012W YCR012W PGK1 PHOSPHOGLYCERATE KINASE YCR016W YCR016W UNKNOWN YCR088W YCR088W ABP1 ACTIN BINDING PROTEIN YCR107W YCR107W AAD3 HYPOTHETICAL ARYL-ALCOHOL DEHYDROGENASE YDL024C YDL024C UNKNOWN; SIMILAR TO ACID PHOSPHATASES YDL027C YDL027C UNKNOWN YDL063C YDL063C UNKNOWN YDL109C YDL109C UNKNOWN YDL112W YDL112W TRM3 TRNA ROBOSE METHYLASE YDL130W YDL130W RPP1B RIBOSOMAL PROTEIN L44', ACIDIC YDL149W YDL149W UNKNOWN YDL184C YDL184C RPL41A RIBOSOMAL PROTEIN L41A YDL200C YDL200C MGT1 6-O-METHYLGUANINE-DNA METHYLASE YDL204W YDL204W UNKNOWN YDL207W YDL207W GLE1 UNKNOWN YDL208W YDL208W NHP2 UNKNOWN; SIMILAR TO HIGH MOBILITY GROUP YDL222C YDL222C UNKNOWN; SIMILAR TO SUR7P YDL243C YDL243C AAD4 HYPOTHETICAL ARYL-ALCOHOL DEHYDROGENASE YDR019C YDR019C GCV1 GLYCINE DECARBOXYLASE T SUBUNIT YDR021W YDR021W FAL1 RNA HELICASE YDR025W YDR025W RPS11A RIBOSOMAL PROTEIN S11A YDR059C YDR059C UBC5 E2 UB.-CONJUGATING ENZYME YDR064W YDR064W RPS13 RIBOSOMAL PROTEIN S13 YDR077W YDR077W SED1 PUTATIVE CELL SURFACE GLYCOPROTEIN YDR085C YDR085C AFR1 CYTOSKELETAL PROTEIN, SIMILAR TO ARRESTI YDR087C YDR087C RRP1 UNKNOWN YDR111C YDR111C UNKNOWN; SIMILAR TO ALANINE AMINOTRANSFE YDR144C YDR144C MKC7 PERIPLASMIC ASPARTYL PROTEASE YDR172W YDR172W SUP35 TRANSLATION RELEASE FACTOR YDR210W YDR210W UNKNOWN YDR211W YDR211W GCD6 TRANSLATION INITIATION FACTOR EIF2B SUBU YDR223W YDR223W UNKNOWN YDR225W YDR225W HTA1 HISTONE H2A YDR226W YDR226W ADK1 CYTOSOLIC ADENYLATE KINASE YDR234W YDR234W LYS4 HOMOACONITASE YDR255C YDR255C UNKNOWN YDR273W YDR273W UNKNOWN YDR280W YDR280W RRP45 3'->5' EXORIBONUCLEASE YDR303C YDR303C UNKNOWN; SIMILAR TO TRANSCRIPTION FACTOR YDR309C YDR309C GIC2 BINDS CDC42P YDR321W YDR321W ASP1 L-ASPARAGINASE I YDR341C YDR341C TRNA SYNTHETASE, ARGININE YDR342C YDR342C HXT7 HEXOSE PERMEASE YDR345C YDR345C HXT3 HEXOSE PERMEASE YDR353W YDR353W TRR1 THIOREDOXIN REDUCTASE YDR374C YDR374C UNKNOWN YDR380W YDR380W UNKNOWN; SIMILAR TO PYRUVATE DECARBOXYLA YDR384C YDR384C UNKNOWN; SIMILAR TO Y. LIPOLYTICA GPR1P YDR391C YDR391C UNKNOWN YDR398W YDR398W UNKNOWN YDR408C YDR408C ADE8 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFER YDR418W YDR418W RPL12B RIBOSOMAL PROTEIN L12B YDR429C YDR429C TIF35 TRANSLATION INITIATION FACTOR EIF3 SUBUN YDR430C YDR430C UNKNOWN; SIMILAR TO CLASS I FAMILY OF AM YDR450W YDR450W RPS18A RIBOSOMAL PROTEIN S18A YDR454C YDR454C GUK1 GUANYLATE KINASE YDR500C YDR500C RPL37B RIBOSOMAL PROTEIN L37B YDR502C YDR502C SAM2 REGULATOR; S-ADENOSYLMETHIONINE SYNTHETA YDR533C YDR533C UNKNOWN YEL012W YEL012W UBC8 E2 UB.-CONJUGATING ENZYME YEL041W YEL041W UNKNOWN; SIMILAR TO FRE2P YEL060C YEL060C PRB1 VACUOLAR PROTEASE B YEL063C YEL063C CAN1 BASIC AMINO ACID PERMEASE YER001W YER001W MNN1 ALPHA-1,3-MANNOSYLTRANSFERASE YER015W YER015W FAA2 ACYL-COA SYNTHETASE YER036C YER036C UNKNOWN; SIMILAR TO MEMBERS OF THE ATP-B YER039C YER039C HVG1 NUCLEOTIDE SUGAR TRANSPORTER (PUTATIVE) YER056C YER056C FCY2 PURINE-CYTOSINE PERMEASE YER062C YER062C HOR2 DL-GLYCEROL-3-PHOSPHATASE YER065C YER065C ICL1 ISOCITRATE LYASE YER082C YER082C UNKNOWN YER084W YER084W UNKNOWN YER101C YER101C AST2 TARGETS PLASMA MEMBRANE ATPASE YER102W YER102W RPS8B RIBOSOMAL PROTEIN S8B YER117W YER117W RPL23B RIBOSOMAL PROTEIN L23B YER156C YER156C UNKNOWN YER162C YER162C RAD4 REPAIROSOME COMPONENT YER181C YER181C UNKNOWN YFL045C YFL045C SEC53 PHOSPHOMANNOMUTASE YFR001W YFR001W UNKNOWN; SIMILAR TO S.POMBE PAD1 PROTEIN YFR032C YFR032C UNKNOWN YFR033C YFR033C QCR6 UBIQUINOL CYTOCHROME-C REDUCTASE SUBUNIT YFR053C YFR053C HXK1 HEXOKINASE I YGL008C YGL008C PMA1 PLASMA MEMBRANE H+-ATPASE YGL047W YGL047W UNKNOWN; SIMILAR TO PLASMODIUM FALCIPARU YGL059W YGL059W UNKNOWN; SIMILAR TO RAT BRANCHED-CHAIN A YGL081W YGL081W UNKNOWN YGL103W YGL103W RPL28 RIBOSOMAL PROTEIN L28 YGL111W YGL111W UNKNOWN YGL121C YGL121C UNKNOWN YGL123W YGL123W RPS2 RIBOSOMAL PROTEIN S2 YGL147C YGL147C RPL9A RIBOSOMAL PROTEIN L9A YGL189C YGL189C RPS26A RIBOSOMAL PROTEIN S26A YGL253W YGL253W HXK2 HEXOKINASE II YGR008C YGR008C STF2 ATPASE STABILIZING FACTOR YGR032W YGR032W GSC2 1,3-BETA-D-GLUCAN SYNTHASE SUBUNIT YGR034W YGR034W RPL26B RIBOSOMAL PROTEIN L26B YGR070W YGR070W ROM1 GDP/GTP EXCHANGE PROTEIN FOR RHO1P YGR079W YGR079W UNKNOWN YGR108W YGR108W CLB1 G2/M CYCLIN YGR111W YGR111W UNKNOWN; SIMILAR TO SOUTHERN HOUSE MOSQU YGR152C YGR152C RSR1 GTP-BINDING PROTEIN, RAS SUPERFAMILY YGR180C YGR180C RNR4 RIBONUCLEOTIDE REDUCTASE YGR189C YGR189C CRH1 UNKNOWN; CELL WALL PROTEIN YGR250C YGR250C UNKNOWN YHL028W YHL028W WSC4 UNKNOWN YHL035C YHL035C UNKNOWN; ATP-BINDING CASSETTE (ABC) SUPE YHL040C YHL040C ARN1 UNKNOWN; SIMILAR TO SUBTELOMERICALLY-ENC YHR016C YHR016C YSC84 UNKNOWN; SIMILAR TO HYPOTHETICAL PROTEIN YHR063C YHR063C UNKNOWN; SIMILAR TO CBS2P YHR097C YHR097C UNKNOWN YHR098C YHR098C SFB3 UNKNOWN; BINDS SED3P AND SEC23P YHR136C YHR136C SPL2 PROTEIN KINASE INHIBITOR YHR138C YHR138C UNKNOWN YHR154W YHR154W ESC4 UNKNOWN YHR170W YHR170W NMD3 NAM7P/UPF1P-INTERACTING PROTEIN YHR176W YHR176W UNKNOWN; SIMILAR TO FLAVIN-CONTAINING MO YHR208W YHR208W BAT1 TRANSAMINASE YIL019W YIL019W UNKNOWN YIL072W YIL072W HOP1 DNA BINDING PROTEIN YIL097W YIL097W UNKNOWN YIL102C YIL102C UNKNOWN YIL117C YIL117C UNKNOWN YIL136W YIL136W OM45 OUTER MITOCHONDRIAL MEMBRANE PROTEIN YIL167W YIL167W SERINE DEHYDRATASE YIR016W YIR016W UNKNOWN YIR030C YIR030C DCG1 MAY BE INVOLVED IN CATABOLITE REPRESSION YJL088W YJL088W ARG3 ORNITHINE CARBAMOYLTRANSFERASE YJR027W YJR027W UNKNOWN; SIMILAR TO E. COLI MOLYBDOPTERI YJR064W YJR064W CCT5 CYTOPLASMIC CHAPERONIN COMPLEX YJR066W YJR066W TOR1 PHOSPHATIDYLINOSITOL 3-KINASE YJR145C YJR145C RPS4A RIBOSOMAL PROTEIN S4A YKL044W YKL044W UNKNOWN YLL055W YLL055W UNKNOWN; SIMILAR TO DAL5P AND MEMBERS OF gene_function SGD_ID YBR183W UNKNOWN S0000387 YCL059C UNKNOWN S0000564 YCR012W GLYCOLYSIS S0000605 YCR016W UNKNOWN S0000609 YCR088W CYTOSKELETON S0000684 YCR107W UNKNOWN S0000704 YDL024C UNKNOWN S0002182 YDL027C UNKNOWN S0002185 YDL063C UNKNOWN S0002221 YDL109C UNKNOWN S0002267 YDL112W TRNA PROCESSING S0002270 YDL130W PROTEIN SYNTHESIS S0002288 YDL149W UNKNOWN S0002308 YDL184C PROTEIN SYNTHESIS S0002343 YDL200C DNA REPAIR S0002359 YDL204W UNKNOWN S0002363 YDL207W MRNA EXPORT S0002366 YDL208W UNKNOWN S0002367 YDL222C UNKNOWN S0002381 YDL243C UNKNOWN S0002402 YDR019C AMINO ACID METABOLISM S0002426 YDR021W RRNA PROCESSING S0002428 YDR025W PROTEIN SYNTHESIS S0002432 YDR059C PROTEIN DEGRADATION, UBIQUITIN-MEDIATED S0002466 YDR064W PROTEIN SYNTHESIS S0002471 YDR077W UNKNOWN S0002484 YDR085C MATING S0002492 YDR087C RRNA PROCESSING S0002494 YDR111C UNKNOWN S0002518 YDR144C PROTEIN DEGRADATION S0002551 YDR172W PROTEIN SYNTHESIS S0002579 YDR210W UNKNOWN S0002618 YDR211W PROTEIN SYNTHESIS S0002619 YDR223W UNKNOWN S0002631 YDR225W CHROMATIN STRUCTURE S0002633 YDR226W METABOLISM S0002634 YDR234W LYSINE BIOSYNTHESIS S0002642 YDR255C UNKNOWN S0002663 YDR273W UNKNOWN S0002681 YDR280W RRNA PROCESSING S0002688 YDR303C UNKNOWN S0002711 YDR309C BUD EMERGENCE S0002717 YDR321W ASPARAGINE UTILIZATION S0002729 YDR341C PROTEIN SYNTHESIS S0002749 YDR342C TRANSPORT S0002750 YDR345C TRANSPORT S0002753 YDR353W PYRIMIDINE METABOLISM S0002761 YDR374C UNKNOWN S0002782 YDR380W UNKNOWN S0002788 YDR384C UNKNOWN S0002792 YDR391C UNKNOWN S0002799 YDR398W UNKNOWN S0002806 YDR408C PURINE BIOSYNTHESIS S0002816 YDR418W PROTEIN SYNTHESIS S0002826 YDR429C PROTEIN SYNTHESIS S0002837 YDR430C UNKNOWN S0002838 YDR450W PROTEIN SYNTHESIS S0002858 YDR454C GUANINE NUCLEOTIDE METABOLISM S0002862 YDR500C PROTEIN SYNTHESIS S0002908 YDR502C METHIONINE BIOSYNTHESIS S0002910 YDR533C UNKNOWN S0002941 YEL012W PROTEIN DEGRADATION, UBIQUITIN-MEDIATED S0000738 YEL041W UNKNOWN S0000767 YEL060C PROTEIN DEGRADATION S0000786 YEL063C TRANSPORT S0000789 YER001W PROTEIN GLYCOSYLATION S0000803 YER015W FATTY ACID METABOLISM S0000817 YER036C UNKNOWN S0000838 YER039C PROTEIN GLYCOSYLATION (PUTATIVE) S0000841 YER056C TRANSPORT S0000858 YER062C GLYCEROL METABOLISM S0000864 YER065C GLYOXYLATE CYCLE S0000867 YER082C UNKNOWN S0000884 YER084W UNKNOWN S0000886 YER101C PLASMA MEMBRANE PROTEIN TARGETING S0000903 YER102W PROTEIN SYNTHESIS S0000904 YER117W PROTEIN SYNTHESIS S0000919 YER156C UNKNOWN S0000958 YER162C DNA REPAIR, NUCLEOTIDE EXCISION S0000964 YER181C UNKNOWN S0000983 YFL045C PROTEIN GLYCOSYLATION S0001849 YFR001W UNKNOWN S0001897 YFR032C UNKNOWN S0001928 YFR033C OXIDATIVE PHOSPHORYLATION S0001929 YFR053C GLYCOLYSIS S0001949 YGL008C H+ HOMEOSTASIS S0002976 YGL047W UNKNOWN S0003015 YGL059W UNKNOWN S0003027 YGL081W UNKNOWN S0003049 YGL103W PROTEIN SYNTHESIS S0003071 YGL111W UNKNOWN S0003079 YGL121C UNKNOWN S0003089 YGL123W PROTEIN SYNTHESIS S0003091 YGL147C PROTEIN SYNTHESIS S0003115 YGL189C PROTEIN SYNTHESIS S0003157 YGL253W GLYCOLYSIS S0003222 YGR008C ATP SYNTHESIS S0003240 YGR032W CELL WALL BIOGENESIS S0003264 YGR034W PROTEIN SYNTHESIS S0003266 YGR070W SIGNALING S0003302 YGR079W UNKNOWN S0003311 YGR108W CELL CYCLE S0003340 YGR111W UNKNOWN S0003343 YGR152C BUD SITE SELECTION S0003384 YGR180C DNA REPLICATION S0003412 YGR189C CELL WALL BIOGENESIS (PUTATIVE) S0003421 YGR250C UNKNOWN S0003482 YHL028W CELL WALL INTEGRITY AND STRESS RESPONSE S0001020 YHL035C UNKNOWN S0001027 YHL040C UNKNOWN S0001032 YHR016C UNKNOWN S0001058 YHR063C UNKNOWN S0001105 YHR097C UNKNOWN S0001139 YHR098C UNKNOWN S0001140 YHR136C CELL CYCLE S0001178 YHR138C UNKNOWN S0001180 YHR154W SILENCING S0001197 YHR170W MRNA DECAY, NONSENSE-MEDIATED S0001213 YHR176W UNKNOWN S0001219 YHR208W BRANCHED CHAIN AMINO ACID DEGRADATION S0001251 YIL019W UNKNOWN S0001281 YIL072W MEIOSIS, SYNAPSIS S0001334 YIL097W UNKNOWN S0001359 YIL102C UNKNOWN S0001364 YIL117C UNKNOWN S0001379 YIL136W (PUTATIVE) MITOCHONDRIAL ORGANIZATION S0001398 YIL167W GLUCONEOGENESIS S0001429 YIR016W UNKNOWN S0001455 YIR030C UNKNOWN S0001469 YJL088W ARGININE BIOSYNTHESIS S0003624 YJR027W UNKNOWN S0003788 YJR064W PROTEIN TARGETING S0003825 YJR066W SIGNALING, CELL CYCLE AND MEIOSIS S0003827 YJR145C PROTEIN SYNTHESIS S0003906 YKL044W UNKNOWN S0001527 YLL055W UNKNOWN S0003978