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1. A method of determining likelihood that a tumour in a patient would be treatable with paclitaxel or a paclitaxel-like drug, the method comprising:
(a) obtaining a gene expression list of a sample of the tumour or an extract of the tumour having message RNA therein of the patient; (b) determining a gene expression profile of the sample from the gene expression list for genes of a gene marker set; and, (c) comparing the gene expression profile of the sample to standardized “good” and “bad” profiles of the marker set to determine whether the gene expression profile of the sample predicts that the tumour is treatable or not treatable with paclitaxel or a paclitaxel-like drug, wherein “good” indicates that the tumour is likely treatable with paclitaxel or a paclitaxel-like drug and “bad” indicates that the tumour is not likely treatable with paclitaxel or a paclitaxel-like drug,and the gene marker set is Set 1, Set 2, Set 3, Set 4, Set 5, Set 6 or a combination thereof, whereinSet 1 consists of:EntrezGene Gene IDFull Name of GeneHELLS 3070Helicase, lymphoid-specificCDC2983Cell division cycle 2, G1 to S and G2 to MPLEKHF179156Pleckstrin homology domain containing, family F (with FYVE domain) member 1IGFBP33486Insulin-like growth factor binding protein 3CASP3 836Caspase 3, apoptosis-related cysteine peptidaseHRK8739 Harakiri, BCL2 interacting protein (contains only BH3 domain)PCSK6 5046Proprotein convertase subtilisin/kexin type 6PLAGL15325Pleiomorphic adenoma gene-like 1NME58382Non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)PROP15626PROP paired-like homeobox 1NOD264127Nucleotide-binding oligomerization domain containing 2CD38952CD38 moleculeATP7A 538ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome)INDO3620 Indoleamine-pyrrole 2,3 dioxygenasePIM211040 Pim-2 oncogeneECT21894Epithelial cell transforming sequence 2 oncogeneCASP8AP29994CASP8 associated protein 2STK17B9262Serine/threonine kinase 17bPRKDC5591Protein kinase, DNA-activated, catalytic polypeptideCRADD8738CASP2 and RIPK1 domain containing adaptor with death domainBECN18678Beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)CAPN1011132Calpain 10PRUNE2158471Prune homolog 2 (Drosophila)SKP26502S-phase kinase-associated protein 2 (p45)ANL125V-abl Abelson murine leukemia viral oncogene homolog 1CLN31201Ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)CTSB1508Cathepsin BMUC24583Mucin 2, oligomeric mucus/gel-formingNUP6223636Nucleoporin 62 kDaAPOE348Apolipoprotein ESet 2 consists of:EntrezGene Gene NameIDFull Name of GeneCENPE1062Centromere protein E, 312 kDaCENPF1063Centromere protein F, 350/400 ka (mitosin)AURKB9212Aurora kinase BTTK7272TTK protein kinaseCDCA855143Cell division cycle associated 8SKP16500S-phase kinase-associated protein 1CCNA2890Cyclin A2CAMK2G818Calcium/calmodulin-dependent protein kinase (CaM kinase) II gammaINHBA3624Inhibin, beta ACDC2983Cell division cycle 2, G1 to S and G2 to MERCC6L54821Excision repair cross-complementing rodent repair deficiency, complementation group 6-likeBUB1B701BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)NCAPD323310Non-SMC condensin II complex, subunit D3CDC25A993Cell division cycle 25 homolog A (S. pombe)DCC179075Defective in sister chromatid cohesion homolog 1 (S. cerevisiae)PSMB95698Proteasome (prosome, macropain) subunit,beta type, 9 (large multifunctional peptidase 2)DLG79787 Discs, large homolog 7 (Drosophila)CHEK11111CHK1 checkpoint homolog (S. pombe)CLASP1 23332Cytoplasmic linker associated protein 1SMC210592Structural maintenance of chromosomes 2ZWINT11130ZW10 interactorSKP26502S-phase kinase-associated protein 2 (p45)NCAPG64151Non-SMC condensin I complex, subunit GDBF410926DBF4 homolog (S. cerevisiae)CDC20991Cell division cycle 20 homolog (S. cerevisiae)STMN13925Stathmin 1/oncoprotein 18MDM24193Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)TXNL4B 54957Thioredoxin-like 4BABL125V-abl Abelson murine leukemia viral oncogene homolog 1NUMA14926Nuclear mitotic apparatus protein 1Set 3 consists of:EntrezGene Gene NameIDFull Name of GeneCCL26347Chemokine (C—C motif) ligand 2TAP16890Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)CD1639332CD163 moleculeIFIH164135Interferon induced with helicase C domain 1SERPINE15054Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1RSAD291543Radical S-adenosyl methionine domain containing 2DHX5879132DEXH (Asp-Glu-X-His) box polypeptide 58VWF7450Von Willebrand factorTNFRSF17608Tumor necrosis factor receptor superfamily, member 17TNFRSF47293Tumor necrosis factor receptor superfamily, member 4PSG95678Pregnancy specific beta-1-glycoprotein 9CCR41233Chemokine (C—C motif) receptor 4FXN2395FrataxinPARP1142Poly (ADP-ribose) polymerase family, member 1C1QB713Complement component 1, q subcomponent, B chainPRKDC5591Protein kinase, DNA-activated, catalytic polypeptideCD38952CD38 moleculeAPOE348Apolipoprotein EFKBP1A 2280FK506 binding protein 1A, 12 kDaIL43565 Interleukin 4PCSK65046Proprotein convertase subtilisin/kexin type 6BECN18678Beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)PSMB95698 Proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2)GALNT22590UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)KLK1326085Kallikrein-related peptidase 13LAX154900Lymphocyte transmembrane adaptor 1GCH12643GTP cyclohydrolase 1 (dopa-responsive dystonia)CLN31201Ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)C2717Complement component 2PSG15669Pregnancy specific beta-1-glycoprotein 1Set 4 consists of:EntrezGene Gene NameIDFull Name of GeneAPI58539Apoptosis inhibitor 5AGT183Angiotensinogen (serpin peptidase inhibitor, clade A, member 8)SAP30BP29115SAP30 binding proteinBNIP3664BCL2/adenovirus E1B 19 kDa interacting protein 3GLI32737GLI-Kruppel family member GLI3 (Greigcephalopolysyndactyly syndrome)UNC5B219699Unc-5 homolog B (C. elegans)PDE1B5153Phosphodiesterase 1B, calmodulin-dependentMSX14487Msh homeobox 1HIP13092Huntingtin interacting protein 1PDCD1011235Programmed cell death 10PPARD5467Peroxisome proliferator-activated receptor LOC283871283871Hypothetical protein LOC283871deltaRRAGA10670Ras-related GTP binding AERBB32065V-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)IHPK251447Inositol hexaphosphate kinase 2EEF1A2 1917Eukaryotic translation elongation factor 1 alpha 2PERP64065PERP, TP53 apoptosis effectorATP6AP1 537ATPase, H+ transporting, lysosomal accessory protein 1ING451147Inhibitor of growth family, member 4NLRP255655NLR family, pyrin domain containing 2FXR18087Fragile X mental retardation, autosomal homolog 1C16orf529965Chromosome 16 open reading frame 5BLCAP10904Bladder cancer associated proteinVEGFA7422Vascular endothelial growth factor AESR12099Estrogen receptor 1TRAF57188TNF receptor-associated factor 5FIS151024Fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)SFRP16422 Secreted frizzled-related protein 1COMP1311 Cartilage oligomeric matrix proteinCDKN2A1029Cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)Set 5 consists of:EntrezGene Gene NameIDFull Name of GenePERP64065PERP, TP53 apoptosis effectorKAL13730Kallmann syndrome 1 sequenceEFS10278Embryonal Fyn-associated substrateCLDN31365Claudin 3CD36948CD36 molecule (thrombospondin receptor)ITGA63655Integrin, alpha 6CXCL126387Chemokine (C—X—C motif) ligand 12(stromal cell-derived factor 1)PCDHB356132Protocadherin beta 3RHOB388Ras homolog gene family, member BITGB13688Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)GMDS2762GDP-mannose 4,6-dehydrataseDLG11739Discs, large homolog 1 (Drosophila)COL19A11310Collagen, type XIX, alpha 1SIGLEC827181Sialic acid binding Ig-like lectin 8PPARD5467Peroxisome proliferator-activated receptor deltaIGFALS 3483 Insulin-like growth factor binding protein, acid labile subunitLAMA43910Laminin, alpha 4STAB123166Stabilin 1PTPRM5797Protein tyrosine phosphatase, receptor type, MSPAM16677Sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)AGT183Angiotensinogen (serpin peptidase inhibitor, clade A, member 8)ZYX7791 ZyxinPCDH75099 Protocadherin 7PCDHGB556101Protocadherin gamma subfamily B, 5MADCAM18174Mucosal vascular addressin cell adhesion molecule 1COMP1311Cartilage oligomeric matrix proteinPVRL25819 Poliovirus receptor-related 2 (herpesvirus entry mediator B)LAMA53911 Laminin, alpha 5PCDHB1754661Protocadherin beta 17 pseudogeneITGA88516 Integrin, alpha 8Set 6 consists of:EntrezGene Gene NameIDFull Name of GenePDE1B5153Phosphodiesterase 1B, calmodulin-dependentITGA63655Integrin, alpha 6CCND1595Cyclin D1DEK7913DEK oncogene (DNA binding)MSX14487Msh homeobox 1CHAF1B8208Chromatin assembly factor 1, subunit B (p60)TLK19874Tousled-like kinase 1SLC25A3655186Solute carrier family 25, member 36RPS6KB16198Ribosomal protein S6 kinase, 70 kDa,polypeptide 1USP17398Ubiquitin specific peptidase 1AGT183Angiotensinogen (serpin peptidase inhibitor, clade A, member 8)PRKRA8575Protein kinase, interferon-inducible double stranded RNA dependent activatorMTMR1522909Myotubularin related protein 15CHRNA31136Cholinergic receptor, nicotinic, alpha 3C16orf529965Chromosome 16 open reading frame 5PPARD5467Peroxisome proliferator-activated receptor deltaFGB2244Fibrinogen beta chainANXA2P2 304Annexin A2 pseudogene 2HSPB1 3315 Heat shock 27 kDa protein 1ANXA2302Annexin A2ESR12099Estrogen receptor 1SMAD2 4087SMAD family member 2STAB1 23166Stabilin 1FANCE2178 Fanconi anemia, complementation group ENFATC44776Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4ERBB3 2065V-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)ERAP151752Endoplasmic reticulum aminopeptidase 1TOR1B 27348Torsin family 1, member B (torsin B)HPS511234Hermansky-Pudlak syndrome 5RPA36119Replication protein A3, 14 kDa |
