Supplementary Fig. 1

A B

Responder_Xenograft_ Responder_Xenograft_ NON- NON- Lu7336, Vehicle vs Lu7466, Vehicle vs Responder_Xenograft_ Responder_Xenograft_ Sagopilone, Welch- Sagopilone, Welch- Lu7187, Vehicle vs Lu7406, Vehicle vs Test: 638 Test: 600 Sagopilone, Welch- Sagopilone, Welch- Test: 468 Test: 482

Responder_Xenograft_ NON- Lu7860, Vehicle vs Responder_Xenograft_ Sagopilone, Welch - Lu7558, Vehicle vs Test: 605 Sagopilone, Welch- Test: 333 Supplementary Fig. 2 Supplementary Fig. 3 Supplementary Figure S1. Venn diagrams comparing probe sets regulated by Sagopilone treatment (10mg/kg for 24h) between individual models (Welsh Test ellipse p-value<0.001 or 5-fold change). A Sagopilone responder models, B Sagopilone non-responder models.

Supplementary Figure S2. Pathway analysis of regulated by Sagopilone treatment in responder xenograft models 24h after Sagopilone treatment by GeneGo Metacore; the most significant pathway map representing cell cycle/spindle assembly and separation is shown, genes upregulated by Sagopilone treatment are marked with red thermometers.

Supplementary Figure S3. GeneGo Metacore pathway analysis of genes differentially expressed between Sagopilone Responder and Non-Responder models displaying –log(p-Values) of most significant pathway maps. Supplementary Tables

Supplementary Table 1. Response and activity in 22 non-small-cell lung cancer (NSCLC) xenograft models after treatment with Sagopilone and other cytotoxic agents commonly used in the management of NSCLC

Tumor Model Response type

Sagopilone Carboplatin Paclitaxel Gemcitabine

Lu7064 PLC R NR R NR Lu7126 SCC NR NR nt R Lu7166 LCC NR NR NR NR Lu7177 SCC R NR NR R Lu7187 PLC NR NR NR R Lu7198 ADC NR NR NR NR tox Lu7298 SCC R NR NR NR Lu7336 PLC R NR R R tox Lu7343 SCC R NR NR R Lu7387 ADC R NR R NR Lu7406 ADC NR NR NR NR Lu7414 SCC R NR NR NR Lu7433 SCC R R R NR Lu7462 ADC R NR NR R Lu7466 ADC R NR R R Lu7506 SCC R R R NR Lu7558 PLC NR R NR R Lu7612 SCC NR R R NR tox Lu7668 DDC R R R Tox Lu7700 ADC R NR NR R Lu7747 SCC NR NR NR NR Lu7860 SCC R NR R NR Overall response 14 (64%) 5 (23%) 9 (43%) 9 (43%) n (%) R, responder (tumor shrinkage and stable disease); NR, non-responder (tumor progression); nt, not tested; tox, toxic; ADC, adenocarcinoma; DDC, dedifferentiated carcinoma; LCC, large cell carcinoma; PLC, pleiomorphic carcinoma; SCC, squamous cell carcinoma Page 2

Supplementary Table 2. Genes regulated only in Sagopilone responder

xenografts 24 hours after a single Sagopilone treatment at p<0.01

A Genes up-regulated after Sagopilone treatment

Ratio of Ratio of P-Value: Means: P-Value: Means: Non- Non- Responde Respon Responde Responde r der r r Xenograft Xenogr Xenograft Xenograft Probe-Set Symbol Gene Description Gene ID s afts s s hypothetical 1553736_at MGC23401 MGC23401 196441 2.24E-05 1.62 3.77E-01 1.10 205235_s_at MPHOSPH1 M-phase phosphoprotein 1 9585 1.35E-04 1.31 5.92E-01 1.06 210527_x_at TUBA2 , alpha 2 7278 4.47E-04 1.20 2.00E-02 1.18 hypothetical protein 225762_x_at LOC284801 LOC284801 284801 5.47E-04 1.39 3.55E-01 1.17 CDC20 cell division cycle 202870_s_at CDC20 20 homolog (S. cerevisiae) 991 6.42E-04 1.40 2.67E-02 1.29 202705_at CCNB2 cyclin B2 9133 7.76E-04 1.31 3.62E-02 1.18 214710_s_at CCNB1 cyclin B1 891 9.08E-04 1.42 2.27E-02 1.20 cyclin-dependent kinase inhibitor 3 (CDK2- associated dual specificity 209714_s_at CDKN3 ) 1033 1.07E-03 1.44 7.53E-01 1.05 open 218542_at C10orf3 reading frame 3 55165 1.10E-03 1.28 4.47E-01 1.11 tubulin, alpha, ubiquitous, 211072_x_at K-ALPHA-1 tubulin, alpha, ubiquitous 10376 1.68E-03 1.10 2.58E-02 1.08 WW domain containing 242427_at WAC adaptor with coiled-coil 51322 1.85E-03 1.38 2.04E-01 1.11 NIMA (never in 204641_at NEK2 gene a)-related kinase 2 4751 2.05E-03 1.32 5.53E-02 1.21 chromosome 15 open 225300_at C15orf23 reading frame 23 90417 2.29E-03 1.30 1.92E-01 1.13 cyclin-dependent kinase inhibitor 3 (CDK2- associated dual specificity 1555758_a_at CDKN3 phosphatase) 1033 2.68E-03 1.39 7.04E-01 1.06 CDC28 protein kinase 204170_s_at CKS2 regulatory subunit 2 1164 2.72E-03 1.27 2.87E-01 1.12 cylicin, basic protein of 216809_at CYLC1 sperm head 1 1538 2.81E-03 1.31 4.46E-01 0.88 226980_at DEPDC1B DEP domain containing 1B 55789 2.86E-03 1.37 6.34E-01 1.07 pituitary tumor-transforming 203554_x_at PTTG1 1 9232 3.43E-03 1.28 3.25E-01 1.11 204444_at KIF11 family member 11 3832 3.78E-03 1.21 8.85E-01 0.99 open 227402_s_at C8orf53 reading frame 53 84294 3.97E-03 1.24 9.37E-02 1.13 218755_at KIF20A kinesin family member 20A 10112 4.11E-03 1.29 4.33E-02 1.16 zinc finger and BTB domain 226284_at ZBTB2 containing 2 57621 4.69E-03 1.14 2.30E-01 1.11 pituitary tumor-transforming 208511_at PTTG3 3 26255 4.91E-03 1.32 6.17E-01 1.06 gb:AI857685 227249_at /DB_XREF=gi:5511301 5.29E-03 1.26 9.60E-02 1.28 Page 3

/DB_XREF=wk96d11.x1 /CLONE=IMAGE:2423253 /FEA=EST /CNT=36 /TID=Hs.263925.3 /TIER=Stack /STK=24 /UG=Hs.263925 /LL=54820 /UG_GENE=FLJ20101 /UG_TITLE=LIS1- interacting ... of inner mitochondrial membrane 9 218316_at TIMM9 homolog (yeast) 26520 5.37E-03 1.20 9.74E-01 1.00 discs, large homolog 7 203764_at DLG7 (Drosophila) 9787 5.75E-03 1.36 5.39E-01 1.12 1570528_at XYLT2 II 64132 5.79E-03 1.84 6.07E-01 0.86 centromere protein A, 204962_s_at CENPA 17kDa 1058 5.87E-03 1.34 1.79E-01 1.14 family with sequence 221591_s_at FAM64A similarity 64, member A 54478 5.95E-03 1.27 1.99E-01 1.13 trophinin associated protein 204649_at TROAP (tastin) 10024 6.24E-03 1.25 5.27E-02 1.16 open 221907_at C14orf172 reading frame 172 115708 6.26E-03 1.19 8.89E-01 0.98 hypothetical protein 1559002_at LOC340544 LOC340544 340544 6.54E-03 1.20 7.05E-01 0.97 hypothetical protein 220060_s_at FLJ20641 FLJ20641 55010 6.58E-03 1.27 9.39E-01 1.01 209464_at AURKB aurora kinase B 9212 7.53E-03 1.26 8.50E-01 1.02 proline/serine-rich coiled- 201896_s_at PSRC1 coil 1 84722 7.67E-03 1.26 2.20E-01 1.12 Homo sapiens, clone 1569958_at IMAGE:4064953, mRNA 8.43E-03 1.75 7.66E-01 0.95 213599_at OIP5 Opa interacting protein 5 11339 8.84E-03 1.29 5.37E-01 1.07 gb:AL133269 /DB_XREF=gi:9662888 /FEA=DNA /CNT=1 /TID=Hs.302112.0 /TIER=ConsEnd /STK=0 /UG=Hs.302112 /UG_TITLE= DNA sequence from clone RP3- 468K3 on chromosome 6q25-26. Contains a beta 216475_at tubulin ... 8.97E-03 1.24 3.91E-01 1.09 218848_at WDR58 WD repeat domain 58 79228 9.16E-03 1.27 9.48E-01 1.01 209408_at KIF2C kinesin family member 2C 11004 9.23E-03 1.20 1.15E-01 1.14 209118_s_at TUBA3 tubulin, alpha 3 7846 9.36E-03 1.53 1.31E-01 1.55 238156_at RPS6 Ribosomal protein S6 6194 9.41E-03 1.27 4.39E-02 1.15 ELK4, ETS-domain protein 206919_at ELK4 (SRF accessory protein 1) 2005 9.86E-03 1.24 6.99E-01 0.92

Page 4

B Genes down-regulated after Sagopilone treatment

Ratio of Ratio of P-Value: Means: P-Value: Means: Non- Non- Responde Respon Responde Responde Entrez r der r r Gene Gen Xenograft Xenogr Xenograft Xenograft Probe-Set Symbol Gene Description e ID s afts s s 241520_x_at KLHL15 Kelch-like 15 (Drosophila) 80311 1.90E-05 0.76 9.54E-01 1.01 Vitamin K epoxide reductase 238305_at VKORC1L1 complex, subunit 1-like 1 154807 6.06E-04 0.47 4.63E-01 0.83 Hypothetical gene supported 1558504_at LOC440721 by AK024248; AL137733 440721 1.09E-03 0.79 5.93E-01 1.06 POU domain, class 5, 1, POU domain, class 5, transcription factor 1 pseudogene 1, similar to POU domain, class LOC441628 5, transcription factor 1 : POU5F1 : (Octamer-binding 441628, 210905_x_at POU5F1P1 transcription factor ... 5460, 5462 1.32E-03 0.57 2.88E-01 0.78 hypothetical protein 243047_at FLJ10404 FLJ10404 54540 1.37E-03 0.64 1.81E-01 0.80 217207_s_at BTNL3 butyrophilin-like 3 10917 1.46E-03 0.74 7.77E-01 0.96 1561589_a_ at NBEAL1 neurobeachin-like 1 65065 1.50E-03 0.76 6.38E-01 1.05 Peptidylprolyl domain and WD repeat 236999_at PPWD1 containing 1 23398 1.81E-03 0.57 6.69E-01 0.90 232410_at RCOR3 REST corepressor 3 55758 1.88E-03 0.75 6.48E-01 0.94 zyg-11 homolog B (C. 202456_s_at ZYG11BL elegans)-like 10444 1.90E-03 0.60 9.85E-01 1.01 DEAD (Asp-Glu-Ala-Asp) box 1558120_at DDX3X polypeptide 3, X-linked 1654 1.94E-03 0.57 7.63E-01 0.96 gb:AF119896.1 /DB_XREF=gi:7770228 /FEA=FLmRNA /CNT=3 /TID=Hs.283978.0 /TIER=FL /STK=0 /UG=Hs.283978 /DEF=Homo sapiens PRO2751 mRNA, complete cds. /PROD=PRO2751 224030_s_at /FL=gb:AF119896.1 2.30E-03 0.55 4.72E-02 0.67 hypothetical gene supported 1557466_at FLJ31104 by AK055666; BC039324 441072 2.30E-03 0.63 6.22E-01 0.93 Homo sapiens, clone 243656_at IMAGE:4581955 2.35E-03 0.78 4.52E-01 1.12 1558698_at ZNF264 zinc finger protein 264 9422 2.39E-03 0.49 2.06E-01 0.69 RP3- hypothetical protein 1562641_at 473B4.1 BC017868 159091 2.51E-03 0.64 7.61E-01 1.06 Full length insert cDNA clone 244292_at ZD83B06 2.53E-03 0.79 1.87E-01 1.13 gb:AL134420 /DB_XREF=gi:6602607 /DB_XREF=DKFZp547F085_ s1 /CLONE=DKFZp547F085 1557315_a_ /TID=Hs2.254128.1 /CNT=6 at /FEA=mRNA /TIER=ConsEnd 2.66E-03 0.56 7.29E-01 0.91 Page 5

/STK=1 /UG=Hs.254128 /UG_TITLE=Homo sapiens cDNA FLJ39920 fis, clone S ... hypothetical protein 237320_at LOC346653 LOC346653 346653 2.67E-03 0.55 5.82E-02 0.61 myeloid/lymphoid or mixed- lineage leukemia (trithorax homolog, Drosophila), 1565254_s_ elongation factor RNA at ELL : MLL polymerase II 4297, 8178 2.68E-03 0.57 6.71E-01 0.94 239631_at FLJ43505 FLJ43505 protein 400823 2.84E-03 0.67 9.93E-01 1.00 GTF2I repeat domain 215569_at GTF2IRD2 containing 2 84163 2.97E-03 0.68 6.69E-01 0.93 213898_at RBM9 RNA binding motif protein 9 23543 3.15E-03 0.70 5.48E-01 0.91 sarcoglycan, beta (43kDa -associated 205121_at SGCB ) 6443 3.24E-03 0.50 4.78E-02 0.73 olfactory receptor, family 2, subfamily L, member 1 1567242_at OR2L1P pseudogene 26247 3.42E-03 0.67 6.98E-01 0.93 NIMA (never in mitosis gene 213328_at NEK1 a)-related kinase 1 4750 3.57E-03 0.79 2.99E-01 0.90 Mitogen-activated protein 216765_at MAP2K5 kinase kinase 5 5607 3.70E-03 0.58 7.00E-01 0.93 myeloid/lymphoid or mixed- 1565436_s_ lineage leukemia (trithorax at MLL homolog, Drosophila) 4297 3.72E-03 0.70 2.47E-01 1.23 240744_at CPA5 carboxypeptidase A5 93979 3.90E-03 0.60 1.58E-01 0.73 235729_at ZNF514 zinc finger protein 514 84874 3.93E-03 0.78 9.67E-01 1.00 235716_at Transcribed 4.16E-03 0.81 5.18E-01 0.90 209146_at SC4MOL sterol-C4-methyl oxidase-like 6307 4.18E-03 0.77 1.74E-02 0.85 EH domain binding protein 1- 1557749_at EHBP1L1 like 1 254102 4.41E-03 0.75 8.57E-01 1.03 4D interacting protein 215575_at PDE4DIP (myomegalin) 9659 4.88E-03 0.64 4.78E-01 1.20 CDNA clone IMAGE:5311336, with 1557571_at apparent retained intron 5.27E-03 0.52 4.56E-01 0.81 Chromosome 10 open 232230_at C10orf75 reading frame 75 90271 5.41E-03 0.70 2.78E-01 0.85 1555347_at KIAA0251 KIAA0251 protein 23042 5.55E-03 0.71 1.19E-02 0.84 229920_at Transcribed locus 5.55E-03 0.74 1.46E-01 1.19 NudE nuclear distribution gene E homolog like 1 (A. 242642_at NDEL1 nidulans) 81565 5.68E-03 0.69 4.57E-01 0.91 unc-84 homolog A (C. 212074_at UNC84A elegans) 23353 5.97E-03 0.87 8.76E-01 0.98 239453_at FNBP1 Formin binding protein 1 23048 6.07E-03 0.75 1.17E-01 0.83 215151_at DOCK10 dedicator of cytokinesis 10 55619 6.20E-03 0.46 5.02E-02 0.56 234534_at MAOA Monoamine oxidase A 4128 6.29E-03 0.69 5.13E-01 0.89 Chromosome 15 open 217548_at C15orf38 reading frame 38 348110 6.54E-03 0.83 5.56E-01 0.95 Basic leucine zipper nuclear 239032_at BLZF1 factor 1 (JEM-1) 8548 6.63E-03 0.75 7.10E-01 0.93 gb:BC017814.1 1565131_x_ /DB_XREF=gi:17389567 at /TID=Hs2.407234.1 /CNT=1 6.76E-03 0.78 8.60E-01 0.97 Page 6

/FEA=mRNA /TIER=ConsEnd /STK=0 /UG=Hs.407234 /UG_TITLE=Homo sapiens, clone IMAGE:4248929, mRNA /DEF=Homo sapiens, clone IMAGE:4248929, mRNA. gb:AA625847 /DB_XREF=gi:2538234 /DB_XREF=zu92a07.s1 /CLONE=IMAGE:745428 /FEA=EST /CNT=5 /TID=Hs.174934.0 /TIER=ConsEnd /STK=5 /UG=Hs.174934 237494_at /UG_TITLE=ESTs 6.84E-03 0.77 7.31E-01 0.96 A kinase (PRKA) anchor 240495_at AKAP1 protein 1 8165 7.06E-03 0.73 6.79E-01 0.92 1554316_at PGLS 6-phosphogluconolactonase 25796 7.07E-03 0.81 2.07E-01 0.90 , cytoplasmic, 224616_at DNCLI2 intermediate polypeptide 2 1783 7.10E-03 0.87 4.20E-01 0.93 Spastic paraplegia 20, spartin 241292_at SPG20 (Troyer syndrome) 23111 7.14E-03 0.57 8.22E-01 0.95 211589_at PML promyelocytic leukemia 5371 7.18E-03 0.61 8.99E-01 0.97 ADP-ribosylation factor 1566476_at ARFGAP3 GTPase activating protein 3 26286 7.19E-03 0.77 2.15E-01 1.25 RAB6A, member RAS 1564820_at RAB6A oncogene family 5870 7.27E-03 0.70 8.70E-01 0.97 243865_x_at GPC6 Glypican 6 10082 7.32E-03 0.56 8.75E-01 1.06 bone morphogenetic protein receptor, type II 231873_at BMPR2 (serine/threonine kinase) 659 7.46E-03 0.84 4.31E-01 0.91 1561067_at PB1 Polybromo 1 55193 7.56E-03 0.64 4.02E-01 0.84 open 236913_at C17orf76 reading frame 76 388341 7.60E-03 0.84 1.24E-01 0.87 NIMA (never in mitosis gene a)-related kinase 1, NIMA (never in mitosis gene a)- 211086_x_at NEK1 related kinase 1 4750 7.60E-03 0.65 3.23E-01 0.86 221195_at LOC51136 PTD016 protein 51136 7.64E-03 0.73 8.91E-02 0.81 pre-B-cell leukemia 230536_at PBX4 transcription factor 4 80714 7.65E-03 0.64 9.79E-01 0.99 PREDICTED: Homo sapiens similar to Hypothetical protein KIAA0563 (LOC440457), 206088_at mRNA 7.66E-03 0.69 5.05E-01 0.88 203567_s_at TRIM38 tripartite motif-containing 38 10475 7.95E-03 0.86 6.74E-01 0.84 Caspase recruitment domain 241884_at CARD4 family, member 4 10392 8.10E-03 0.74 3.64E-01 1.15 232163_at WDR19 WD repeat domain 19 57728 8.14E-03 0.69 5.24E-01 0.89 scavenger receptor class B, 201646_at SCARB2 member 2 950 8.17E-03 0.76 5.52E-01 0.91 Isoleucine-tRNA synthetase 240234_at IARS2 2, mitochondrial 55699 8.18E-03 0.83 8.44E-01 0.98 pleckstrin homology, Sec7 and coiled-coil domains 202879_s_at PSCD1 1(cytohesin 1) 9267 8.22E-03 0.68 4.88E-01 0.87 PDZ domain containing RING 212915_at PDZRN3 finger 3 23024 8.39E-03 0.48 9.89E-02 2.11 Page 7

signal transducer and activator of transcription 3 (acute-phase response 208992_s_at STAT3 factor) 6774 8.69E-03 0.87 6.81E-01 0.96 ataxia telangiectasia mutated (includes complementation 210858_x_at ATM groups A, C and D) 472 8.73E-03 0.77 3.78E-02 0.83 family with sequence 202915_s_at FAM20B similarity 20, member B 9917 8.89E-03 0.88 5.93E-01 0.95 glycine-, glutamate-, thienylcyclohexylpiperidine- 243696_at GlyBP binding protein 9731 8.99E-03 0.62 3.51E-01 0.88 aryl hydrocarbon receptor 233724_at ARNT nuclear translocator 405 9.04E-03 0.68 4.29E-01 0.89 hypothetical protein 1563827_at LOC158434 LOC158434 158434 9.07E-03 0.50 5.91E-01 1.19 216847_at KIAA1660 KIAA1660 protein 85374 9.08E-03 0.74 2.68E-01 1.20 chromosome 8 open reading 220216_at C8orf44 frame 44 56260 9.29E-03 0.81 6.98E-01 1.05 , gamma 2, smooth 202274_at ACTG2 muscle, enteric 72 9.48E-03 0.78 4.27E-02 0.85 Wiskott-Aldrich syndrome 38964_r_at WAS (eczema-thrombocytopenia) 7454 9.56E-03 0.76 3.27E-01 0.89 open reading 243350_at C5orf15 frame 15 56951 9.63E-03 0.79 5.55E-01 0.95 ATP-binding cassette, sub- family C (CFTR/MRP), 244053_at ABCC4 member 4 10257 9.76E-03 0.64 7.96E-01 0.96 215156_at WDR61 WD repeat domain 61 80349 9.84E-03 0.86 3.71E-01 0.91

p-values <1.00 E-3 and fold-changes above 1.3 are shaded Page 8

Supplementary Table 3. Genes regulated only in Sagopilone non-responder

xenografts 24 hours after a single Sagopilone treatment at p<0.01

A Genes up-regulated after Sagopilone treatment

Ratio of Ratio of P-Value: Means: P-Value: Means: Non- Non- Responde Responde Responde Responde r r r r Gene Entrez Xenograft Xenograft Xenograft Xenograft Probe-Set Symbol Gene Description Gene ID s s s s 228729_at CCNB1 cyclin B1 891 1.30E-02 1.42 5.83E-04 1.34 synaptosomal-associated protein, 204953_at SNAP91 91kDa homolog (mouse) 9892 9.73E-01 0.99 7.35E-04 2.18 215137_at KIAA0508 KIAA0508 protein 57244 2.05E-01 0.82 8.07E-04 1.90 212786_at KIAA0350 KIAA0350 protein 23274 6.89E-01 0.96 1.10E-03 1.33 216837_at EPHA5 EPH receptor A5 2044 8.93E-01 1.02 2.38E-03 1.90 TNFAIP8L , alpha-induced 227420_at 1 protein 8-like 1 126282 1.40E-01 1.16 2.85E-03 1.23 Nucleolar and spindle associated 1562163_at NUSAP1 protein 1 51203 6.40E-01 1.11 4.14E-03 1.98 207330_at PZP pregnancy-zone protein 5858 8.76E-01 1.03 4.44E-03 1.82 218829_s_a chromodomain helicase DNA binding t CHD7 protein 7 55636 4.84E-01 1.05 4.50E-03 1.21 228522_at KIAA1545 Myc target 1 57666 6.32E-01 0.90 5.19E-03 1.76 201997_s_a spen homolog, transcriptional t SPEN regulator (Drosophila) 23013 9.27E-01 1.01 6.08E-03 1.19 dual specificity phosphatase 3 (vaccinia virus phosphatase VH1- 201536_at DUSP3 related) 1845 6.68E-01 0.98 8.29E-03 1.18 244530_at FLJ25422 Hypothetical protein FLJ25422 202151 3.16E-01 0.84 8.69E-03 1.63

B Genes down-regulated after Sagopilone treatment

Ratio of Ratio of P-Value: Means: P-Value: Means: Non- Non- Responde Responde Responde Responde Entrez r r r r Gene Gene Xenograft Xenograft Xenograft Xenograft Probe-Set Symbol Gene Description ID s s s s 206481_s_ at LDB2 LIM domain binding 2 9079 3.34E-01 0.73 3.21E-04 0.34 1553215_s 22101 _at CCDC7 coiled-coil domain containing 7 6 3.30E-01 0.84 9.65E-04 0.56 gb:AK092487.1 /DB_XREF=gi:21751096 /TID=Hs2.379113.1 /CNT=21 /FEA=mRNA /TIER=Stack /STK=8 /UG=Hs.379113 /UG_TITLE=Homo sapiens cDNA FLJ35168 fis, clone 1556030_ PLACE6012604. /DEF=Homo sapiens at cDNA FLJ3516 ... 8.24E-01 0.97 1.04E-03 0.78 237925_at Transcribed locus 8.61E-01 1.03 1.38E-03 0.47 Page 9

1554478_ a_at FLJ20718 hypothetical protein FLJ20718 55027 6.57E-01 0.95 1.59E-03 0.73 211392_s_ at ZNF278 zinc finger protein 278 23598 2.26E-01 1.11 1.65E-03 0.84 209131_s_ synaptosomal-associated protein, at SNAP23 23kDa 8773 6.81E-01 0.97 2.09E-03 0.79 242150_at Transcribed locus 6.44E-01 0.95 2.75E-03 0.76 230461_s_ Melanoma associated antigen at MUM1 (mutated) 1 84939 2.63E-01 0.91 3.02E-03 0.76 1557878_ Homo sapiens, clone at IMAGE:5184785, mRNA 7.09E-01 1.04 3.14E-03 0.78 1558723_ 28401 at LOC284014 hypothetical protein LOC284014 4 4.21E-01 0.89 3.28E-03 0.74 235672_at MAP6 -associated protein 6 4135 6.91E-01 1.10 3.68E-03 0.40 216665_s_ at TTTY2 testis-specific transcript, Y-linked 2 60439 7.67E-02 0.64 3.88E-03 0.40 CAP-binding protein complex 233600_at FLJ23588 interacting protein 1 64800 4.22E-01 0.87 4.32E-03 0.62 mediator of RNA polymerase II 219318_x_ transcription, subunit 31 homolog at MED31 (yeast) 51003 5.98E-01 1.04 4.50E-03 0.80 1564965_ Breast carcinoma amplified sequence at BCAS1 1 8537 9.51E-01 0.98 5.02E-03 0.43 1561609_ at CDNA clone IMAGE:6161060 2.94E-02 0.78 5.17E-03 0.68 DKFZp564H hypothetical gene supported by 44043 234787_at 213 AL049275 2 3.63E-01 0.84 5.30E-03 0.47 methylesterase 224094_at PPME1 1 51400 7.18E-01 1.07 5.60E-03 0.54 25363 228495_at CCDC75 Coiled-coil domain containing 75 5 7.74E-01 1.02 5.63E-03 0.83 1563253_s v-erb-b2 erythroblastic leukemia viral _at ERBB3 oncogene homolog 3 (avian) 2065 5.57E-01 0.93 6.01E-03 0.72 gb:AW627948 /DB_XREF=gi:7374738 /DB_XREF=hi36c09.x1 /CLONE=IMAGE:2974384 /FEA=EST /CNT=4 /TID=Hs.129557.0 /TIER=ConsEnd /STK=4 241085_at /UG=Hs.129557 /UG_TITLE=ESTs 1.80E-01 1.29 6.21E-03 0.53 Acyl-CoA synthetase bubblegum 241941_at ACSBG2 family member 2 81616 1.05E-01 0.81 6.36E-03 0.78 gb:AA521463 /DB_XREF=gi:2262006 /DB_XREF=aa69f03.s1 /CLONE=IMAGE:826205 /FEA=EST /CNT=8 /TID=Hs.183424.0 /TIER=ConsEnd /STK=4 240335_at /UG=Hs.183424 /UG_TITLE=ESTs 3.08E-02 0.83 6.82E-03 0.65 1569469_ 43170 a_at LHX8 LIM homeobox 8 7 4.93E-01 0.84 7.35E-03 0.44 cutaneous T-cell lymphoma- 220957_at CTAGE1 associated antigen 1 64693 3.19E-01 0.92 7.65E-03 0.60 28555 227466_at LOC285550 hypothetical protein LOC285550 0 4.97E-01 1.07 8.42E-03 0.87 1552825_ 25288 at ZNF396 zinc finger protein 396 4 6.07E-01 0.90 8.46E-03 0.54 215649_s_ mevalonate kinase (mevalonic at MVK aciduria) 4598 4.44E-01 0.92 8.92E-03 0.75 205369_x_ dihydrolipoamide branched chain at DBT transacylase E2 1629 8.87E-01 0.99 8.93E-03 0.80 Page 10

224105_x_ at Clone FLB8034 PRO2158 3.43E-01 0.90 9.22E-03 0.72 p-values <1.00 E-3 and fold-changes above 1.3 are shaded

Supplementary Table 4. GeneGo Metacore Pathway analysis on genes regulated by Sagopilone in NSCLC Xenografts

A Pathways regulated by Sagopilone in Responder models

Objects Objects in # Map Cell Process p-Value from List in Map Map Spindle assembly and Cell cycle 2.41E-10 10 32 separation 2 Role of APC in cell cycle regulation Cell cycle 3.79E-05 6 32 3 Role of Nek in cell cycle regulation Cell cycle 2.77E-04 5 29 4 The metaphase checkpoint Cell cycle 6.42E-03 4 36 5 Gap junctions Cell adhesion/Transport 1.05E-02 3 22 6 Initiation of mitosis Cell cycle 1.51E-02 3 25 7 Role of CDK5 in neuronal development Development/Neurogenesis 2.69E-02 3 31 8 Angiopoietin - Tie2 signaling Development/Angiogenesis 3.43E-02 3 34 Chromosome condensation in 9 Cell cycle 6.67E-02 2 20 prometaphase 10 Sister chromatid cohesion Cell cycle 7.27E-02 2 21

B Pathways regulated by Sagopilone in Non-responder models

Objects Objects in # Map Cell Process p-Value from List in Map Map Leucune, isoleucine and valine 1 Aminoacid 1.94E-01 1 13 metabolism Nucleocytoplasmic transport of 2 Cell cycle 2.08E-01 1 14 CDK/Cyclins 3 Propionate metabolism p.1 metabolism 2.34E-01 1 16 Propionate metabolism p.1 / Human 4 Carbohydrates metabolism 2.47E-01 1 17 version wtCFTR and delta508 traffic / Clathrin 5 coated vesicles formation (norm and Cystic fibrosis 2.72E-01 1 19 CF) Chromosome condensation in 6 Cell cycle 2.84E-01 1 20 prometaphase 7 Cell cycle (generic schema) Cell cycle 2.96E-01 1 21 8 Sister chromatid cohesion Cell cycle 2.96E-01 1 21 9 Cholesterol Biosynthesis metabolism 2.96E-01 1 21 Development/Neurogenesis/ ACM3 activation of astroglial cells 10 G-protein coupled receptor 2.96E-01 1 21 proliferation signaling Page 11

Supplementary Table 5. Genes differentially expressed between Sagopilone

Responder and Non-Responder models at baseline (PBS treated samples), at

minimum p-value 10-5 and minimum fold-change of 1.5.

A Genes with higher expression levels in Sagopilone Non-Responder models

Gene Ratio of Probe Set ID Symbol Gene Description Entrez Gene ID means P-Value 218434_s_at AACS acetoacetyl-CoA synthetase 65985 1.72 2.82E-06 acyl-CoA synthetase short-chain family 234801_s_at ACSS1 member 1 84532 4.72 5.09E-09 223638_at AE2 hypothetical protein AE2 84224 1.70 2.36E-06 204333_s_at AGA aspartylglucosaminidase 175 1.79 1.53E-05 204499_at AGTPBP1 ATP/GTP binding protein 1 23287 2.04 6.14E-05 225342_at AK3L1 adenylate kinase 3-like 1 205 1.67 9.89E-05 201952_at ALCAM activated leukocyte cell adhesion molecule 214 2.46 7.30E-06 aldehyde dehydrogenase 6 family, 204289_at ALDH6A1 member A1 4329 2.35 9.05E-06 208212_s_at ALK anaplastic lymphoma kinase (Ki-1) 238 2.31 3.68E-05 215783_s_at ALPL , liver/bone/kidney 249 2.53 4.58E-05 212286_at ANKRD12 repeat domain 12 23253 1.64 8.69E-05 227337_at ANKRD37 ankyrin repeat domain 37 353322 2.03 4.10E-06 226228_at AQP4 4 361 8.56 2.04E-07 ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A- 236742_at ARFGEF1 inhibited) 10565 1.60 1.90E-05 Rho guanine nucleotide exchange factor 218501_at ARHGEF3 (GEF) 3 50650 1.54 6.39E-07 Rho guanine nucleotide exchange factor 228596_at ARHGEF5 (GEF) 5 7984 1.95 1.74E-06 N-acylsphingosine amidohydrolase (acid 213702_x_at ASAH1 ceramidase) 1 427 1.51 9.10E-06 214934_at ATP9B ATPase, Class II, type 9B 374868 1.76 4.78E-06 235240_at ATXN3 Ataxin 3 4287 2.06 2.27E-06 222780_s_at BAALC brain and acute leukemia, cytoplasmic 79870 2.62 6.40E-05 209502_s_at BAIAP2 BAI1-associated protein 2 10458 1.97 2.70E-06 218264_at BCCIP BRCA2 and CDKN1A interacting protein 56647 1.66 4.37E-06 blocked early in transport 1 homolog (S. 220470_at BET1L cerevisiae)-like 51272 1.69 8.28E-05 BCL2/adenovirus E1B 19kDa interacting protein 3-like, BCL2/adenovirus E1B 221479_s_at BNIP3L 19kDa interacting protein 3-like 665 1.77 2.49E-07 207722_s_at BTBD2 BTB (POZ) domain containing 2 55643 1.56 4.89E-06 218456_at C1QDC1 C1q domain containing 1 65981 1.82 6.82E-05 C1q and tumor necrosis factor related protein 3, C1q and tumor necrosis factor 220988_s_at C1QTNF3 related protein 3 114899 1.92 4.14E-08 214164_x_at CA12 carbonic anhydrase XII 771 6.28 3.44E-06 205199_at CA9 carbonic anhydrase IX 768 3.06 1.04E-05 calmodulin regulated -associated 212711_at CAMSAP1 protein 1 157922 1.70 1.79E-11 1552326_a_at CCDC11 coiled-coil domain containing 11 220136 2.84 1.97E-05 227191_at CDA08 T-cell immunomodulatory protein 81533 1.75 7.08E-06 Cell division cycle 42 (GTP binding protein, 1556931_at CDC42 25kDa) 998 1.58 8.69E-05 231170_at CDKL5 Cyclin-dependent kinase-like 5 6792 2.09 6.88E-05 Page 12

cyclin-dependent kinase inhibitor 2D (p19, 210240_s_at CDKN2D inhibits CDK4) 1032 1.70 1.19E-05 CDP-diacylglycerol synthase 233630_at CDS2 (phosphatidate cytidylyltransferase) 2 8760 1.54 1.49E-05 CCAAT/enhancer binding protein (C/EBP), 213006_at CEBPD delta 1052 2.34 8.57E-05 carboxyl ester (bile salt-stimulated 1553970_s_at CEL lipase) 1056 4.22 5.57E-05 225542_at CENTB5 centaurin, beta 5 116983 1.59 4.32E-06 213509_x_at CES2 carboxylesterase 2 (intestine, liver) 8824 1.82 2.85E-05 cystic fibrosis transmembrane conductance regulator, ATP-binding 205043_at CFTR cassette (sub-family C, member 7) 1080 3.63 5.01E-05 225817_at CGNL1 cingulin-like 1 84952 3.03 1.44E-05 chromodomain helicase DNA binding 225026_at CHD6 protein 6 84181 1.53 2.28E-05 CK2 interacting protein 1; HQ0024c 218223_s_at CKIP-1 protein 51177 3.62 3.03E-07 221328_at CLDN17 claudin 17 26285 2.49 8.39E-05 201561_s_at CLSTN1 calsyntenin 1 22883 1.84 1.10E-08 CCR4-NOT transcription complex, subunit 210203_at CNOT4 4 4850 1.56 3.05E-05 CCR4-NOT transcription complex, subunit 1552344_s_at CNOT7 7 29883 1.74 4.86E-08 229426_at COX5A cytochrome c oxidase subunit Va 9377 1.54 1.30E-05 cysteine rich transmembrane BMP 202551_s_at CRIM1 regulator 1 (chordin-like) 51232 2.23 1.27E-06 206315_at CRLF1 cytokine receptor-like factor 1 9244 2.78 3.94E-05 220090_at CRNN cornulin 49860 4.10 4.56E-05 204573_at CROT carnitine O-octanoyltransferase 54677 1.91 5.55E-05 205489_at CRYM crystallin, mu 1428 3.91 1.76E-07 and spindle pole associated 220072_at CSPP1 protein 1 79848 1.53 5.69E-07 211126_s_at CSRP2 cysteine and glycine-rich protein 2 1466 2.91 3.20E-05 Cut-like 1, CCAAT displacement protein 1566243_at CUTL1 (Drosophila) 1523 1.99 1.79E-06 cytochrome P450, family 2, subfamily C, 215103_at CYP2C18 polypeptide 18 1562 7.86 3.43E-07 Cytochrome P450, family 2, subfamily C, 216661_x_at CYP2C9 polypeptide 9 1559 3.59 9.11E-08 cytochrome P450, family 2, subfamily R, 227109_at CYP2R1 polypeptide 1 120227 2.78 8.92E-05 dishevelled associated activator of 216060_s_at DAAM1 morphogenesis 1 23002 2.16 1.88E-07 228329_at DAB1 Disabled homolog 1 (Drosophila) 1600 7.16 1.50E-07 degenerative spermatocyte homolog 2, 236496_at DEGS2 lipid desaturase (Drosophila) 123099 3.19 7.96E-05 214247_s_at DKK3 dickkopf homolog 3 (Xenopus laevis) 27122 5.54 9.86E-05 discs, large homolog 3 (neuroendocrine- 212728_at DLG3 dlg, Drosophila) 1741 2.11 2.83E-05 doublesex and mab-3 related transcription 223704_s_at DMRT2 factor 2 10655 6.70 4.18E-05 DnaJ (Hsp40) homolog, subfamily B, 200666_s_at DNAJB1 member 1 3337 1.64 2.39E-05 DnaJ (Hsp40) homolog, subfamily B, 209015_s_at DNAJB6 member 6 10049 1.78 1.12E-05 200762_at DPYSL2 dihydropyrimidinase-like 2 1808 2.50 3.23E-05 230395_at DREV1 DORA reverse strand protein 1 51108 1.62 4.31E-05 236511_at DUSP16 Dual specificity phosphatase 16 80824 2.10 2.21E-07 Dynein, cytoplasmic 1, intermediate chain 242363_at DYNC1I2 2 1781 1.96 8.17E-06 EGF-like repeats and discoidin I-like 207379_at EDIL3 domains 3 10085 3.06 2.29E-06 Page 13

226869_at EGFL3 EGF-like-domain, multiple 3 1953 3.16 6.67E-05 eukaryotic initiation factor 2- 218696_at EIF2AK3 alpha kinase 3 9451 1.59 2.62E-06 201436_at EIF4E eukaryotic translation initiation factor 4E 1977 1.58 1.30E-05 ELAV (embryonic lethal, abnormal vision, 227746_at ELAVL1 Drosophila)-like 1 (Hu antigen R) 1994 1.58 2.00E-05 ELK4, ETS-domain protein (SRF 206919_at ELK4 accessory protein 1) 2005 1.56 8.03E-05 Homo sapiens, clone IMAGE:3459231, mRNA, Echinoderm microtubule 1569086_at EML2 associated protein like 2 24139 2.10 8.41E-05 243016_at ENOSF1 Enolase superfamily member 1 55556 1.94 3.78E-07 erythrocyte band 4.1- 206710_s_at EPB41L3 like 3 23136 12.56 2.18E-05 erythrocyte membrane protein band 4.1 220524_at EPB41L4B like 4B 54566 2.22 1.44E-06 erythrocyte membrane protein band 4.9 204505_s_at EPB49 (dematin) 2039 2.29 1.15E-07 227449_at EPHA4 EPH receptor A4 2043 3.96 1.25E-09 230425_at EPHB1 EPH receptor B1 2047 7.37 3.28E-05 233979_s_at ESPN 83715 2.53 2.23E-05 239227_at EXT1 Exostoses (multiple) 1 2131 1.69 1.58E-07 243652_at EYA2 Eyes absent homolog 2 (Drosophila) 2139 2.30 1.34E-05 coagulation factor III (thromboplastin, 204363_at F3 ) 2152 2.36 2.41E-11 family with sequence similarity 3, member 227676_at FAM3D D 131177 4.67 3.44E-06 family with sequence similarity 43, member 1558174_at FAM43A A 131583 2.66 3.53E-05 family with sequence similarity 57, member 218898_at FAM57A A 79850 2.12 1.37E-05 family with sequence similarity 62 (C2 224698_at FAM62B domain containing) member B 57488 1.57 7.99E-06 Family with sequence similarity 64, 230076_at FAM64A member A 54478 2.18 5.33E-06 FERM, RhoGEF and pleckstrin domain 204511_at FARP2 protein 2 9855 1.81 1.96E-06 FAT tumor suppressor homolog 1 201579_at FAT (Drosophila) 2195 2.07 4.51E-06 227641_at FBXL16 F-box and leucine-rich repeat protein 16 146330 2.02 9.68E-05 FBXO16 : 232693_s_at ZNF395 zinc finger protein 395, F-box protein 16 157574, 55893 2.08 7.73E-06 1552721_a_at FGF1 fibroblast growth factor 1 (acidic) 2246 2.84 3.07E-05 205110_s_at FGF13 fibroblast growth factor 13 2258 3.86 8.97E-05 218614_at FLJ10652 hypothetical protein FLJ10652 55196 1.70 5.64E-05 FLJ11000 : hypothetical protein FLJ11000, 1561894_at MGC5242 hypothetical protein MGC5242 55281, 78996 1.62 5.77E-05 218610_s_at FLJ11151 hypothetical protein FLJ11151 55313 2.83 7.40E-05 46142_at FLJ12681 hypothetical protein FLJ12681 64788 2.35 9.26E-07 219135_s_at FLJ12681 hypothetical protein FLJ12681 64788 2.72 3.64E-05 242838_at FLJ12748 hypothetical protein FLJ12748 79929 1.64 2.48E-07 1560599_a_at FLJ14640 hypothetical protein FLJ14640 84902 1.77 2.78E-06 233651_s_at FLJ14981 hypothetical protein FLJ14981 84954 2.30 2.70E-10 218692_at FLJ20366 hypothetical protein FLJ20366 55638 2.31 8.30E-05 240046_at FLJ25778 Hypothetical protein FLJ25778 254048 1.56 1.35E-05 1553311_at FLJ33860 hypothetical protein FLJ33860 284756 3.45 4.01E-05 1558212_at FLJ35024 hypothetical LOC401491 401491 2.32 1.22E-06 239483_at FLJ37035 FLJ37035 protein 399821 2.22 8.69E-05 6 (neurotransmitter transporter, creatine), member 8, similar to FLJ43855 : sodium- and chloride-dependent creatine 215812_s_at SLC6A8 transporter 386757, 6535 2.79 3.76E-05 Page 14

244552_at FLJ46419 FLJ46419 protein 388507 5.20 7.27E-11 209471_s_at FNTA farnesyltransferase, CAAX box, alpha 2339 1.51 6.46E-06 1568865_at FNTB Farnesyltransferase, CAAX box, beta 2342 1.82 8.45E-07 228188_at FOSL2 FOS-like antigen 2 2355 1.51 4.11E-05 244845_at FOXP1 Forkhead box P1 27086 1.92 7.00E-06 220910_at FRAS1 Fraser syndrome 1 80144 2.03 8.82E-05 3 (galactoside 3(4)-L- fucosyltransferase, Lewis blood group 214088_s_at FUT3 included) 2525 2.86 8.22E-09 fucosyltransferase 6 (alpha (1,3) 211885_x_at FUT6 fucosyltransferase) 2528 3.71 2.68E-11 204451_at FZD1 frizzled homolog 1 (Drosophila) 8321 2.65 2.21E-05 UDP-N-acetyl-alpha-D- galactosamine:polypeptide N- acetylgalactosaminyltransferase 7 222587_s_at GALNT7 (GalNAc-T7) 51809 1.73 1.06E-05 UDP-N-acetyl-alpha-D- galactosamine:polypeptide N- 1554079_at GALNTL4 acetylgalactosaminyltransferase-like 4 374378 2.61 2.85E-09 Glyceraldehyde-3-phosphate 222280_at GAPDHS dehydrogenase, spermatogenic 26330 1.76 4.48E-07 210002_at GATA6 GATA binding protein 6 2627 2.45 2.16E-05 218912_at GCC1 GRIP and coiled-coil domain containing 1 79571 1.54 1.76E-06 Growth hormone inducible transmembrane 1564148_at GHITM protein 27069 2.38 3.21E-05 Glutamic-oxaloacetic transaminase 1, 1568190_at GOT1 soluble (aspartate aminotransferase 1) 2805 3.15 3.01E-07 234194_at GPC3 Glypican 3 2719 2.99 3.52E-05 1561195_at GPR137B G protein-coupled receptor 137B 7107 2.49 3.45E-05 G protein-coupled receptor, family C, 203632_s_at GPRC5B group 5, member B 51704 4.43 3.96E-07 215248_at GRB10 growth factor receptor-bound protein 10 2887 2.45 7.87E-06 204396_s_at GRK5 G protein-coupled receptor kinase 5 2869 3.59 4.08E-14 G1 to S phase transition 2, G1 to S phase 205541_s_at GSPT2 transition 2 23708 6.73 2.40E-05 214521_at HES2 hairy and enhancer of split 2 (Drosophila) 54626 2.50 3.03E-07 218780_at HOOK2 hook homolog 2 (Drosophila) 29911 1.50 9.16E-05 240527_at HOOK3 Hook homolog 3 (Drosophila) 84376 2.06 7.66E-07 v-Ha-ras Harvey rat sarcoma viral 212983_at HRAS oncogene homolog 3265 1.98 1.64E-07 insulin-like growth factor binding protein 2, 202718_at IGFBP2 36kDa 3485 8.42 2.03E-05 inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex- 202490_at IKBKAP associated protein 8518 1.57 4.00E-05 inhibitor of kappa light polypeptide gene 209341_s_at IKBKB enhancer in B-cells, kinase beta 3551 1.58 3.95E-06 228287_at ING5 inhibitor of growth family, member 5 84289 1.81 4.35E-06 227432_s_at INSR 3643 2.40 4.28E-05 201656_at ITGA6 integrin, alpha 6 3655 2.89 2.22E-08 1554306_at ITPKB inositol 1,4,5-trisphosphate 3-kinase B 3707 2.01 5.62E-05 1558447_at JMJD2B Jumonji domain containing 2B 23030 2.48 4.31E-06 229139_at JPH1 junctophilin 1 56704 2.53 4.66E-05 potassium voltage-gated channel, 210036_s_at KCNH2 subfamily H (eag-related), member 2 3757 2.63 4.11E-08 236783_at KCNIP4 Kv channel interacting protein 4 80333 2.89 3.92E-09 , subfamily K, member 204678_s_at KCNK1 1 3775 2.41 4.90E-05 potassium large conductance calcium- activated channel, subfamily M, alpha 221584_s_at KCNMA1 member 1 3778 2.61 8.16E-06 Page 15

243435_at KCNQ1OT1 KCNQ1 overlapping transcript 1 10984 3.29 7.34E-09 potassium voltage-gated channel, delayed- 205968_at KCNS3 rectifier, subfamily S, member 3 3790 3.71 5.13E-07 202417_at KEAP1 kelch-like ECH-associated protein 1 9817 2.71 8.44E-05 KH domain containing, RNA binding, 209781_s_at KHDRBS3 signal transduction associated 3 10656 4.47 2.35E-05 228325_at KIAA0146 KIAA0146 protein 23514 2.32 7.61E-05 239946_at KIAA0922 KIAA0922 protein 23240 1.67 8.04E-05 242846_at KIAA1217 KIAA1217 56243 2.84 7.30E-05 233823_at KIAA1276 KIAA1276 protein 27146 2.98 4.14E-08 223497_at KIAA1411 KIAA1411 57579 2.11 3.91E-06 230492_s_at KIAA1434 hypothetical protein KIAA1434 56261 2.18 4.53E-06 227091_at KIAA1505 KIAA1505 protein 57639 1.90 5.67E-09 227228_s_at KIAA1509 KIAA1509 440193 2.08 9.05E-06 226494_at KIAA1543 KIAA1543 57662 1.95 4.62E-05 1563621_at KIAA1706 KIAA1706 protein 80820 2.14 5.72E-05 221778_at KIAA1718 KIAA1718 protein 80853 2.15 6.38E-08 236255_at KIAA1909 KIAA1909 protein 153478 4.64 1.82E-07 220782_x_at KLK12 kallikrein 12 43849 2.74 2.42E-05 210306_at L3MBTL l(3)mbt-like (Drosophila) 26013 1.84 4.86E-05 LA16c- 1557835_at 360B4.1 Hypothetical protein FLJ12681 64788 3.90 1.09E-06 La ribonucleoprotein domain family, 231824_at LARP2 member 2 55132 1.61 7.86E-05 likely ortholog of mouse limb-bud and heart gene, likely ortholog of mouse limb- 221011_s_at LBH bud and heart gene 81606 3.26 3.00E-06 222506_at LMBR1 limb region 1 homolog (mouse) 64327 1.67 3.98E-06 218574_s_at LMCD1 LIM and cysteine-rich domains 1 29995 2.01 7.85E-05 227569_at LNX2 ligand of numb-protein X 2 222484 1.70 1.55E-05 1558412_at LOC113230 hypothetical protein LOC113230 113230 1.75 2.99E-06 1553890_s_at LOC126147 hypothetical protein BC018697 126147 2.73 1.55E-05 239150_at LOC132203 similar to hypothetical protein A430083B19 132203 4.27 7.03E-11 1552986_at LOC142937 hypothetical protein BC008131 142937 1.58 3.90E-05 228080_at LOC143903 layilin 143903 4.58 9.84E-05 227951_s_at LOC147965 hypothetical protein LOC147965 147965 1.57 3.23E-06 1555898_at LOC150759 Hypothetical protein LOC150759 150759 1.93 4.94E-05 1554542_at LOC153328 similar to CG4995 gene product 153328 1.60 5.66E-06 227868_at LOC154761 hypothetical protein LOC154761 154761 1.99 6.00E-05 213776_at LOC157562 hypothetical protein LOC157562 157562 1.65 5.86E-05 1569156_at LOC162993 hypothetical protein LOC162993 162993 3.32 9.97E-09 227037_at LOC201164 similar to CG12314 gene product 201164 1.62 8.13E-05 239609_s_at LOC254531 PLSC domain containing protein 254531 1.55 6.40E-05 226382_at LOC283070 hypothetical protein LOC283070 283070 2.63 5.21E-05 1556425_a_at LOC284219 hypothetical protein LOC284219 284219 2.04 3.06E-05 1556638_at LOC284530 hypothetical protein LOC284530 284530 2.95 2.98E-05 1563088_a_at LOC284837 hypothetical protein LOC284837 284837 2.81 4.00E-06 225034_at LOC286167 hypothetical protein LOC286167 286167 2.97 8.69E-07 226395_at LOC286170 hypothetical protein LOC286170 286170 1.64 1.63E-05 232182_at LOC286272 hypothetical protein LOC286272 286272 2.11 7.32E-05 236933_at LOC388353 hypothetical LOC388353 388353 2.11 1.90E-05 1556814_a_at LOC388890 Hypothetical LOC388890 388890 1.53 5.41E-05 236181_at LOC389831 Hypothetical gene supported by AL713796 389831 2.27 4.52E-05 213556_at LOC390940 similar to R28379_1 390940 3.73 2.03E-06 LOC401363 : Hypothetical protein FLJ25037, 243009_at LOC402530 Hypothetical LOC441242 401363, 402530 1.92 2.07E-08 Page 16

1557293_at LOC440993 hypothetical gene supported by AK128346 440993 1.92 5.99E-05 LOC441485 kinase, alpha 2 (liver), 209438_at : PHKA2 LOC441485 441485, 5256 1.57 6.61E-06 1554803_s_at LOC493829 similar to tripartite motif-containing 4 493829 2.34 5.45E-05 224180_x_at LOC51057 hypothetical protein LOC51057 51057 1.55 1.93E-06 203897_at LOC57149 hypothetical protein A-211C6.1 57149 1.64 8.21E-05 207797_s_at LRP2BP LRP2 binding protein 55805 2.29 5.13E-05 223552_at LRRC4 leucine rich repeat containing 4 64101 4.29 1.05E-06 LSM8 homolog, U6 small nuclear RNA 235470_at LSM8 associated (S. cerevisiae) 51691 1.81 4.98E-07 242024_at LUC7L2 LUC7-like 2 (S. cerevisiae) 51631 1.85 1.64E-05 V-maf musculoaponeurotic fibrosarcoma 229327_s_at MAF oncogene homolog (avian) 4094 3.68 4.43E-05 v-maf musculoaponeurotic fibrosarcoma 222670_s_at MAFB oncogene homolog B (avian) 9935 3.49 2.62E-05 223313_s_at MAGED4 melanoma antigen family D, 4 81557 14.93 6.12E-09 1566597_at MAPK10 Mitogen-activated protein kinase 10 5602 3.79 3.09E-06 membrane-associated ring finger (C3HC4) 213256_at MARCH3 3 115123 3.72 4.45E-09 1559045_at MCC Mutated in colorectal cancers 4163 2.15 1.64E-05 Microcephaly, primary autosomal 1557347_at MCPH1 recessive 1 79648 2.15 1.07E-05 207159_x_at MECT1 mucoepidermoid carcinoma translocated 1 23373 1.51 4.23E-05 major facilitator superfamily domain 225316_at MFSD2 containing 2 84879 2.09 4.64E-05 225861_at MGC15416 hypothetical protein MGC15416 84331 1.60 2.41E-06 217438_at MGC29898 Hypothetical protein MGC29898 133015 2.30 2.16E-05 218953_s_at MGC3265 hypothetical protein MGC3265 78991 1.61 6.05E-05 229302_at MGC33926 hypothetical protein MGC33926 130733 4.40 9.65E-06 241987_x_at MGC39715 hypothetical protein MGC39715 169166 7.11 6.46E-06 227459_at MGC5242 Hypothetical protein MGC5242 78996 1.55 2.88E-06 209845_at MKRN1 makorin, ring finger protein, 1 23608 1.73 2.14E-05 Myeloid/lymphoid or mixed-lineage 235217_at MLL5 leukemia 5 (trithorax homolog, Drosophila) 55904 1.51 2.90E-05 224866_at MLSTD2 male sterility domain containing 2 84188 1.81 6.88E-06 1558014_s_at MLSTD2 male sterility domain containing 2 84188 1.91 3.87E-05 203878_s_at MMP11 matrix metallopeptidase 11 (stromelysin 3) 4320 1.93 4.51E-06 membrane protein, palmitoylated 7 1564308_a_at MPP7 (MAGUK p55 subfamily member 7) 143098 2.02 3.49E-07 226256_at MRPS22 mitochondrial ribosomal protein S22 56945 2.19 6.54E-07 242732_at MTSS1 Metastasis suppressor 1 9788 1.98 9.70E-05 202364_at MXI1 MAX interactor 1, MAX interactor 1 4601 1.66 7.07E-05 215074_at MYO1B IB 4430 1.80 3.56E-09 217297_s_at MYO9B myosin IXB 4650 1.63 9.66E-06 NADH dehydrogenase (ubiquinone) 1 beta 202839_s_at NDUFB7 subcomplex, 7, 18kDa 4713 1.50 1.64E-06 206089_at NELL1 NEL-like 1 (chicken) 4745 7.15 6.34E-06 nuclear factor of activated T-cells, 211105_s_at NFATC1 cytoplasmic, -dependent 1 4772 1.98 3.81E-05 237001_at NIBP NIK and IKK{beta} binding protein 83696 1.56 5.52E-05 NK3 transcription factor related, locus 1 209706_at NKX3-1 (Drosophila) 4824 2.34 8.23E-11 215743_at NMT2 N-myristoyltransferase 2 9397 1.56 9.29E-05 Notch homolog 1, translocation-associated 218902_at NOTCH1 (Drosophila) 4851 1.67 3.59E-05 thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) NR1D1 : oncogene homolog, avian), nuclear 31637_s_at THRA receptor subfamily 1, group D, member 1 7067, 9572 1.68 1.43E-06 204760_s_at NR1D1 : thyroid hormone receptor, alpha 7067, 9572 2.21 3.35E-08 Page 17

THRA (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian), nuclear receptor subfamily 1, group D, member 1 nuclear receptor subfamily 1, group D, 209750_at NR1D2 member 2 9975 1.89 1.64E-06 nuclear receptor subfamily 1, group D, 225768_at NR1D2 member 2 9975 1.81 4.81E-06 208241_at NRG1 neuregulin 1 3084 3.31 3.18E-05 210683_at NRTN neurturin 4902 3.85 2.82E-06 229838_at NUCB2 nucleobindin 2 4925 2.10 8.17E-07 1553847_a_at NURIT testis-specific leucine zipper protein nurit 220082 1.58 7.18E-05 213273_at ODZ4 odz, odd Oz/ten-m homolog 4 (Drosophila) 26011 4.96 2.61E-05 Oxoglutarate (alpha-ketoglutarate) 229449_at OGDH dehydrogenase (lipoamide) 4967 2.13 8.33E-05 procollagen-proline, 2-oxoglutarate 4- dioxygenase (proline 4-hydroxylase), alpha 207543_s_at P4HA1 polypeptide I 5033 1.77 2.81E-06 p21/Cdc42/Rac1-activated kinase 1 209615_s_at PAK1 (STE20 homolog, yeast) 5058 2.27 3.19E-06 50400_at PAOX polyamine oxidase (exo-N4-amino) 196743 2.26 4.80E-09 228569_at PAPOLA poly(A) polymerase alpha 10914 1.87 9.19E-05 Par-3 partitioning defective 3 homolog (C. 237782_at PARD3 elegans) 56288 1.73 5.64E-07 poly (ADP-ribose) polymerase family, 229138_at PARP11 member 11 57097 2.92 1.31E-05 207059_at PAX9 paired box gene 9 5083 2.95 3.00E-06 228905_at PCM1 Pericentriolar material 1 5108 2.07 1.75E-05 Protein-L-isoaspartate (D-aspartate) O- 238902_at PCMTD1 methyltransferase domain containing 1 115294 1.53 2.52E-05 214175_x_at PDLIM4 PDZ and LIM domain 4 8572 4.53 3.52E-07 232304_at PELI1 Pellino homolog 1 (Drosophila) 57162 2.34 7.30E-07 213469_at PGAP1 GPI deacylase 80055 2.50 5.28E-05 204525_at PHF14 PHD finger protein 14 9678 1.72 6.91E-06 209439_s_at PHKA2 phosphorylase kinase, alpha 2 (liver) 5256 1.75 1.09E-07 243032_at PIP3-E Phosphoinositide-binding protein PIP3-E 26034 2.11 8.17E-05 239124_at PITPNA Phosphatidylinositol transfer protein, alpha 5306 1.53 4.99E-05 paired-like homeodomain transcription 209587_at PITX1 factor 1 5307 6.93 1.13E-09 235746_s_at PLA2R1 A2 receptor 1, 180kDa 22925 4.44 3.86E-06 , beta 1 211925_s_at PLCB1 (phosphoinositide-specific) 23236 2.92 3.99E-09 Phospholipase C, beta 1 242494_at PLCB1 (phosphoinositide-specific) 23236 2.67 7.39E-12 tumor necrosis factor receptor superfamily, member 25, pleckstrin homology domain PLEKHG5 : containing, family G (with RhoGef domain) 210847_x_at TNFRSF25 member 5 57449, 8718 2.15 7.87E-06 215412_x_at PMS2L2 postmeiotic segregation increased 2-like 2 5380 1.54 4.02E-06 209147_s_at PPAP2A phosphatidic type 2A 8611 1.83 5.31E-06 210946_at PPAP2A phosphatidic acid phosphatase type 2A 8611 1.83 4.06E-06 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting 214978_s_at PPFIA4 protein (liprin), alpha 4 8497 2.66 2.73E-05 (formerly 2A), regulatory subunit B (PR 52), alpha 228013_at PPP2R2A isoform 5520 1.64 6.74E-06 protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform 207000_s_at PPP3CC (calcineurin A gamma) 5533 1.73 1.33E-08 PRB1 : proline-rich protein BstNI subfamily 1, PRB2 : proline-rich protein BstNI subfamily 3, 440083, 5542, 206998_x_at PRB3 : proline-rich protein BstNI subfamily 4, 5544, 5545 1.99 6.01E-06 Page 18

PRB4 proline-rich protein BstNI subfamily 2 39729_at PRDX2 peroxiredoxin 2 7001 1.75 1.57E-06 226069_at PRICKLE1 prickle-like 1 (Drosophila) 144165 2.78 2.64E-05 225197_at PRO0149 PRO0149 protein 29035 1.66 2.90E-06 PRSS1 : PRSS2 : , serine, 1 (trypsin 1), protease, PRSS3 : serine, 2 (trypsin 2), protease, serine, 3 154754, 5644, 216470_x_at TRY6 (mesotrypsin), C 5645, 5646 4.27 1.19E-05 205402_x_at PRSS2 protease, serine, 2 (trypsin 2) 5645 5.17 5.88E-05 207463_x_at PRSS3 protease, serine, 3 (mesotrypsin) 5646 3.53 4.54E-05 218613_at PSD3 pleckstrin and Sec7 domain containing 3 23362 1.87 3.32E-06 230380_at PSRC2 Proline/serine-rich coiled-coil 2 196441 1.61 6.77E-05 1552848_a_at PTCHD1 patched domain containing 1 139411 3.82 2.67E-06 phosphatase and tensin homolog (mutated 233314_at PTEN in multiple advanced cancers 1) 5728 2.17 9.57E-06 protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated 204201_s_at PTPN13 phosphatase) 5783 2.24 9.76E-05 Protein tyrosine phosphatase, receptor 234224_at PTPRG type, G 5793 4.09 7.63E-07 1557938_s_at PTRF polymerase I and transcript release factor 284119 1.89 2.70E-05 234998_at RAB11A RAB11A, member RAS oncogene family 8766 1.65 8.48E-07 208732_at RAB2 RAB2, member RAS oncogene family 5862 1.52 2.56E-08 208733_at RAB2 RAB2, member RAS oncogene family 5862 2.20 6.51E-10 229072_at RAB30 RAB30, member RAS oncogene family 27314 2.04 8.06E-05 225001_at RAB3D RAB3D, member RAS oncogene family 9545 1.69 3.65E-07 233385_x_at RAB4B RAB4B, member RAS oncogene family 53916 1.99 3.25E-06 201048_x_at RAB6A RAB6A, member RAS oncogene family 5870 1.56 1.11E-05 ral guanine nucleotide dissociation 209051_s_at RALGDS stimulator 5900 1.52 4.40E-06 230233_at RASGEF1B RasGEF domain family, member 1B 153020 4.32 6.69E-07 retinol dehydrogenase 12 (all-trans and 9- 242998_at RDH12 cis) 145226 2.45 2.55E-05 238017_at RDHE2 epidermal retinal dehydrogenase 2 195814 4.30 2.02E-08 223468_s_at RGMA RGM domain family, member A 56963 2.78 2.56E-05 233811_at RIN2 Ras and Rab interactor 2 54453 2.37 8.37E-07 220991_s_at RNF32 ring finger protein 32, ring finger protein 32 140545 2.40 1.37E-05 206050_s_at RNH1 / inhibitor 1 6050 1.56 1.20E-07 roundabout, axon guidance receptor, 226766_at ROBO2 homolog 2 (Drosophila) 6092 4.39 2.74E-05 208646_at RPS14 ribosomal protein S14 6208 1.83 8.88E-08 1560021_at RPS20 Ribosomal protein S20 6224 2.68 6.96E-06 208903_at RPS28 Ribosomal protein S28 6234 1.62 5.42E-05 239863_at RRM2 Ribonucleotide reductase M2 polypeptide 6241 1.56 5.36E-06 235354_s_at RSRC1 Arginine/serine-rich coiled-coil 1 51319 1.89 8.56E-05 239496_at RSU1 Ras suppressor protein 1 6251 1.67 1.61E-06 212425_at SCAMP1 Secretory carrier membrane protein 1 9522 1.59 2.43E-05 serologically defined colon cancer antigen 227785_at SDCCAG8 8 10806 3.36 3.09E-08 serum deprivation response 222717_at SDPR (phosphatidylserine binding protein) 8436 6.89 2.72E-09 235974_at SEC8L1 SEC8-like 1 (S. cerevisiae) 60412 1.80 8.48E-05 1555851_s_at SEPW1 selenoprotein W, 1 6415 1.55 3.74E-06 stress-associated 200969_at SERP1 protein 1 27230 1.52 2.95E-10 signaling intermediate in Toll pathway, 218225_at SITPEC evolutionarily conserved 51295 1.77 1.91E-09 solute carrier family 16 (monocarboxylic 227506_at SLC16A9 acid transporters), member 9 220963 4.77 7.36E-06 Page 19

solute carrier family 1 (glutamate/neutral 212810_s_at SLC1A4 transporter), member 4 6509 2.72 7.61E-05 Solute carrier family 25 (mitochondrial 231145_at SLC25A21 oxodicarboxylate carrier), member 21 89874 4.82 2.16E-05 solute carrier family 2 (facilitated glucose 201249_at SLC2A1 transporter), member 1 6513 2.38 9.93E-05 228486_at SLC44A1 solute carrier family 44, member 1 23446 2.43 3.09E-05 solute carrier family 6 (neurotransmitter 202219_at SLC6A8 transporter, creatine), member 8 6535 4.62 2.20E-06 solute carrier family 6 (neurotransmitter 210854_x_at SLC6A8 transporter, creatine), member 8 6535 2.78 2.94E-05 Solute carrier family 9 (sodium/hydrogen 226125_at SLC9A3 exchanger), member 3 6550 5.19 5.24E-11 232481_s_at SLITRK6 SLIT and NTRK-like family, member 6 84189 2.54 7.45E-05 SMAD, mothers against DPP homolog 1 227798_at SMAD1 (Drosophila) 4086 1.93 4.90E-06 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 241756_at SMARCA2 subfamily a, member 2 6595 2.26 8.63E-06 sphingomyelin phosphodiesterase, acid- 213624_at SMPDL3A like 3A 10924 3.81 4.94E-07 218788_s_at SMYD3 SET and MYND domain containing 3 64754 1.51 3.07E-05 226683_at SNAG1 associated golgi protein 1 112574 1.67 8.37E-08 small nuclear RNA activating complex, 204104_at SNAPC2 polypeptide 2, 45kDa 6618 1.54 5.28E-07 Staphylococcal domain 232525_at SND1 containing 1 27044 1.70 2.02E-06 227878_s_at SPATA11 spermatogenesis associated 11 84266 2.03 2.13E-11 215833_s_at SPPL2B signal peptidase-like 2B 56928 1.53 7.83E-05 serine palmitoyltransferase, long chain 1554053_at SPTLC1 base subunit 1 10558 1.76 9.02E-06 SLIT-ROBO Rho GTPase activating 232954_at SRGAP3 protein 3 9901 2.29 9.11E-06 222844_s_at SRR serine racemase 63826 1.57 8.27E-07 210829_s_at SSBP2 single-stranded DNA binding protein 2 23635 2.60 4.18E-06 229744_at SSFA2 Sperm specific antigen 2 6744 2.74 1.89E-05 ST3 beta-galactoside alpha-2,3- 208322_s_at ST3GAL1 1 6482 2.84 8.66E-06 236931_at STIM1 Stromal interaction molecule 1 6786 2.49 2.89E-05 241860_at STK17B Basic leucine zipper and W2 domains 1 9262 2.20 2.28E-07 241473_at SULF1 1 23213 4.87 5.42E-07 203998_s_at SYT1 synaptotagmin I 6857 3.55 1.22E-05 227134_at SYTL1 synaptotagmin-like 1 84958 2.21 2.52E-05 203386_at TBC1D4 TBC1 domain family, member 4 9882 1.69 2.85E-05 transcription factor 3 (E2A immunoglobulin 210776_x_at TCF3 enhancer binding factors E12/E47) 6929 1.60 3.62E-06 transglutaminase 3 (E polypeptide, protein- 206004_at TGM3 glutamine-gamma-glutamyltransferase) 7053 6.61 4.99E-05 translocase of inner mitochondrial 203092_at TIMM44 membrane 44 homolog (yeast) 10469 1.54 7.03E-08 TIMP metallopeptidase inhibitor 3 (Sorsby 201150_s_at TIMP3 fundus dystrophy, pseudoinflammatory) 7078 10.21 2.65E-05 transducin-like enhancer of split 4 (E(sp1) 235765_at TLE4 homolog, Drosophila) 7091 3.03 8.48E-06 227393_at TMEM16J transmembrane protein 16J 338440 1.78 3.76E-05 230467_at TMEM52 transmembrane protein 52 339456 1.91 3.99E-05 226483_at TMEM68 transmembrane protein 68 137695 1.62 2.69E-08 65630_at TMEM80 transmembrane protein 80 283232 1.51 5.26E-05 226553_at TMPRSS2 transmembrane protease, serine 2 7113 5.55 1.15E-06 tumor necrosis factor receptor superfamily, 219423_x_at TNFRSF25 member 25 8718 1.92 1.03E-06 1556116_s_at TNPO1 Transportin 1 3842 3.24 4.08E-07 Page 20

201691_s_at TPD52 tumor protein D52 7163 2.39 4.26E-06 206179_s_at TPPP brain-specific protein p25 alpha 11076 2.41 1.70E-06 translocation associated membrane 202368_s_at TRAM2 protein 2 9697 1.83 7.66E-05 202341_s_at TRIM2 tripartite motif-containing 2 23321 4.43 1.29E-05 227102_at TRIM35 tripartite motif-containing 35 23087 1.74 3.15E-07 1554250_s_at TRIM50B tripartite motif-containing 50B 375593 2.09 9.12E-09 TRIM50B : tripartite motif-containing 50B, tripartite 1554182_at TRIM50C motif-containing 50C 375593, 378108 2.41 7.77E-05 215395_x_at TRY6 trypsinogen C 154754 3.20 4.16E-05 209114_at TSPAN1 tetraspanin 1 10103 3.06 4.97E-05 230244_at UNQ830 ASCL830 389084 2.35 6.20E-05 209822_s_at VLDLR very low density lipoprotein receptor 7436 4.58 3.99E-10 228024_at VPS37A vacuolar protein sorting 37A (yeast) 137492 1.53 2.03E-06 229158_at WNK4 WNK lysine deficient protein kinase 4 65266 3.27 1.18E-05 1556595_at WWOX B-box and SPRY domain containing 51741 1.90 2.48E-05 233677_at XPO5 Exportin 5 57510 1.87 3.03E-06 221646_s_at ZDHHC11 zinc finger, DHHC-type containing 11 79844 3.24 1.16E-07 Zic family member 2 (odd-paired homolog, 223642_at ZIC2 Drosophila) 7546 4.06 1.07E-05 234394_at ZNF124 zinc finger protein 124 (HZF-16) 7678 1.83 3.15E-05 229870_at ZNF143 Zinc finger protein 143 (clone pHZ-1) 7702 1.99 6.25E-05 213916_at ZNF20 zinc finger protein 20 (KOX 13) 7568 1.61 4.37E-08 243940_at ZNF218 zinc finger protein 218 128553 6.38 2.32E-05 212774_at ZNF238 zinc finger protein 238 10472 1.75 3.73E-05 1555337_a_at ZNF317 zinc finger protein 317 57693 1.53 2.29E-05 221123_x_at ZNF395 zinc finger protein 395 55893 1.84 4.18E-06 226202_at ZNF398 zinc finger protein 398 57541 1.56 9.19E-10 215359_x_at ZNF44 zinc finger protein 44 (KOX 7) 51710 1.72 1.84E-07 241731_x_at ZNF440 zinc finger protein 440 126070 1.83 2.60E-05 205928_at ZNF443 zinc finger protein 443 10224 2.49 2.53E-05 1568720_at ZNF506 zinc finger protein 506 91115 2.38 5.70E-05 220709_at ZNF556 zinc finger protein 556 80032 5.25 4.94E-07 228305_at ZNF565 zinc finger protein 565 147929 1.68 1.04E-07 242564_at ZNF587 Zinc finger protein 587 84914 1.92 1.80E-07 1569108_a_at ZNF589 zinc finger protein 589 51385 1.94 7.34E-06 228864_at ZNF653 zinc finger protein 653 115950 1.53 4.07E-05 zinc finger, RAN-binding domain 244092_at ZRANB3 containing 3 84083 1.70 1.75E-05

B Genes with lower expression in Sagopilone Non-Responders

Gene Ratio of Probe Set ID Symbol Gene Description Entrez Gene ID means P-Value 218991_at ABC1 amplified in breast cancer 1 63897 0.61 3.97E-05 ATP-binding cassette, sub-family F (GCN20), member 1, ATP-binding 200045_at ABCF1 cassette, sub-family F (GCN20), member 1 23 0.65 2.52E-11 ATP-binding cassette, sub-family G 209735_at ABCG2 (WHITE), member 2 9429 0.26 1.10E-05 229534_at ACOT4 acyl-CoA 4 122970 0.52 4.84E-06 201786_s_at ADAR adenosine deaminase, RNA-specific 103 0.60 3.65E-06 AE01 : AG1 hypothetical protein DJ328E19.C1.1, 200030, 25832, : hypothetical protein FLJ20719, 284565, 401967, DJ328E19. hypothetical protein LOC200030, 440670, 440673, 214693_x_at C1.1 : hypothetical protein MGC8902, similar to 440675, 55672 0.59 4.51E-07 Page 21

FLJ20719 : KIAA1693 protein, AE01 mRNA, AG1 LOC200030 protein, hypothetical L ... : LOC401967 : LOC440675 : MGC8902 201792_at AEBP1 AE binding protein 1 165 0.39 2.54E-05 AG1 : hypothetical protein FLJ20719, AG1 215434_x_at FLJ20719 protein 440673, 55672 0.65 5.86E-07 202820_at AHR aryl hydrocarbon receptor 196 0.56 1.48E-06 203002_at AMOTL2 angiomotin like 2 51421 0.57 1.96E-06 1553138_a_at ANKRD41 ankyrin repeat domain 41 126549 0.33 3.30E-05 acidic (leucine-rich) nuclear phosphoprotein 32 family, member E, acidic (leucine-rich) nuclear 208103_s_at ANP32E phosphoprotein 32 family, member E 81611 0.59 3.72E-06 alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, 202888_s_at ANPEP microsomal aminopeptidase, CD13, p150) 290 0.14 1.14E-06 anterior pharynx defective 1 homolog A (C. 218389_s_at APH1A elegans) 51107 0.66 5.08E-06 203382_s_at APOE apolipoprotein E 348 0.29 1.61E-05 Aryl hydrocarbon receptor nuclear 231016_s_at ARNT translocator 405 0.63 8.30E-11 239825_at ATF6 Activating transcription factor 6 22926 0.57 2.64E-05 227904_at AZI2 5-azacytidine induced 2 64343 0.62 1.03E-05 UDP-Gal:betaGlcNAc beta 1,4- 210243_s_at B4GALT3 , polypeptide 3 8703 0.53 4.72E-06 225472_at BAT4 HLA-B associated transcript 4 7918 0.63 1.12E-05 214439_x_at BIN1 bridging integrator 1 274 0.29 9.16E-06 218732_at BIT1 Bcl-2 inhibitor of transcription 51651 0.66 8.39E-07 basic leucine zipper nuclear factor 1 (JEM- 203840_at BLZF1 1) 8548 0.65 8.51E-05 219345_at BOLA1 bolA-like 1 (E. coli) 51027 0.59 4.14E-07 bromodomain and WD repeat domain 219280_at BRWD1 containing 1 54014 0.65 5.39E-05 220840_s_at C1orf112 chromosome 1 open reading frame 112 55732 0.56 1.82E-06 232065_x_at C1orf155 chromosome 1 open reading frame 155 91687 0.65 2.95E-05 218932_at C1orf181 chromosome 1 open reading frame 181 54680 0.63 4.84E-06 213872_at C6orf62 open reading frame 62 81688 0.53 1.32E-08 201700_at CCND3 cyclin D3 896 0.49 3.13E-05 chromatin assembly factor 1, subunit B 204775_at CHAF1B (p60) 8208 0.66 7.95E-05 chromodomain helicase DNA binding 212539_at CHD1L protein 1-like 9557 0.60 1.64E-05 235286_at CKLF Chemokine-like factor 51192 0.51 3.51E-07 207855_s_at CLCC1 CLIC-like 1 23155 0.64 1.73E-06 202087_s_at CTSL L 1514 0.18 5.93E-05 211122_s_at CXCL11 chemokine (C-X-C motif) ligand 11 6373 0.31 6.67E-05 227133_at CXorf39 chromosome X open reading frame 39 139231 0.66 3.63E-09 cytochrome P450, family 1, subfamily B, 202437_s_at CYP1B1 polypeptide 1 1545 0.08 2.42E-11 cytochrome P450, family 39, subfamily A, 244407_at CYP39A1 polypeptide 1 51302 0.27 5.08E-05 222958_s_at DEPDC1 DEP domain containing 1 55635 0.60 3.96E-06 47553_at DFNB31 deafness, autosomal recessive 31 25861 0.33 2.57E-05 DEAH (Asp-Glu-Ala-His) box polypeptide 218277_s_at DHX40 40 79665 0.63 1.68E-08 203334_at DHX8 DEAH (Asp-Glu-Ala-His) box polypeptide 8 1659 0.63 4.13E-08 231778_at DLX3 distal-less homeo box 3 1747 0.34 9.13E-06 Page 22

DNA (cytosine-5-)-methyltransferase 3 222640_at DNMT3A alpha 1788 0.59 6.98E-08 down-regulator of transcription 1, TBP- 209188_x_at DR1 binding (negative 2) 1810 0.64 3.94E-08 238508_at DRF1 Dbf4-related factor 1 80174 0.45 3.16E-05 223445_at DTNBP1 dystrobrevin binding protein 1 84062 0.59 1.99E-06 225415_at DTX3L deltex 3-like (Drosophila) 151636 0.66 7.11E-06 DNA segment on chromosome X (unique) 219061_s_at DXS9879E 9879 expressed sequence 8270 0.64 1.38E-07 207231_at DZIP3 zinc finger DAZ interacting protein 3 9666 0.61 5.95E-05 203692_s_at E2F3 E2F transcription factor 3 1871 0.64 2.05E-10 ectonucleotide pyrophosphatase/phosphodiesterase 5 227803_at ENPP5 (putative function) 59084 0.35 4.40E-05 221486_at ENSA endosulfine alpha 2029 0.54 2.07E-05 222262_s_at ETNK1 ethanolamine kinase 1 55500 0.59 4.14E-05 202013_s_at EXT2 exostoses (multiple) 2 2132 0.60 1.22E-05 213689_x_at FAM69A Ribosomal protein L5 388650 0.25 8.02E-06 family with sequence similarity 73, member 243042_at FAM73A A 374986 0.64 7.50E-05 FAM91A2 : family with sequence similarity 91, member 1568609_s_at FLJ39739 A2, FLJ39739 protein 388685, 57234 0.31 1.85E-06 203647_s_at FDX1 ferredoxin 1 2230 0.63 2.20E-05 219774_at FLJ10996 hypothetical protein FLJ10996 54520 0.66 4.40E-06 220467_at FLJ21272 hypothetical protein FLJ21272 80100 0.29 5.60E-06 218248_at FLJ22794 FLJ22794 protein 63901 0.59 9.72E-06 220141_at FLJ23554 hypothetical protein FLJ23554 79864 0.31 6.47E-05 226946_at FLJ30596 hypothetical protein FLJ30596 133686 0.65 5.68E-08 1553611_s_at FLJ33790 hypothetical protein FLJ33790 283212 0.44 3.88E-05 228937_at FLJ38725 hypothetical protein FLJ38725 144811 0.41 6.81E-06 232615_at FLJ39739 FLJ39739 protein 388685 0.38 4.78E-07 204789_at FMNL1 formin-like 1 752 0.37 7.88E-05 FSH primary response (LRPR1 homolog, 214804_at FSHPRH1 rat) 1 2491 0.62 2.96E-07 218103_at FTSJ3 FtsJ homolog 3 (E. coli) 117246 0.66 1.15E-06 guanylate binding protein 2, interferon- 242907_at GBP2 inducible 2634 0.32 2.01E-06 223434_at GBP3 guanylate binding protein 3 2635 0.22 1.69E-05 glycerophosphodiester phosphodiesterase 1560227_at GDPD1 domain containing 1 284161 0.48 3.24E-05 222432_s_at GK001 GK001 protein 57003 0.62 1.63E-06 214430_at GLA galactosidase, alpha 2717 0.57 7.33E-08 229332_at GLOXD1 glyoxalase domain containing 1 84842 0.41 7.71E-05 218350_s_at GMNN geminin, DNA replication inhibitor 51053 0.58 3.45E-06 guanine nucleotide binding protein (G 223487_x_at GNB4 protein), beta polypeptide 4 59345 0.24 5.04E-09 guanine nucleotide binding protein (G 204115_at GNG11 protein), gamma 11 2791 0.18 1.32E-05 227022_at GNPDA2 glucosamine-6-phosphate deaminase 2 132789 0.64 6.38E-05 glucosamine (N-acetyl)-6-sulfatase 212335_at GNS (Sanfilippo disease IIID) 2799 0.60 4.04E-08 209469_at GPM6A glycoprotein M6A 2823 0.24 6.92E-05 207183_at GPR19 G protein-coupled receptor 19 2842 0.40 5.75E-05 G-protein signalling modulator 2 (AGS3- 1557433_at GPSM2 like, C. elegans) 29899 0.65 1.74E-06 227163_at GSTO2 glutathione S- omega 2 119391 0.25 3.04E-06 202947_s_at GYPC (Gerbich blood group) 2995 0.44 8.44E-05 1557169_x_at HCG11 HLA complex group 11 493812 0.21 3.58E-09 202814_s_at HEXIM1 hexamethylene bis-acetamide inducible 1 10614 0.61 3.33E-09 Page 23

211329_x_at HFE hemochromatosis 3077 0.59 5.10E-08 215933_s_at HHEX hematopoietically expressed homeobox 3087 0.49 6.78E-05 HIST1H2B 235681_at D Histone 1, H2bd 3017 0.49 1.54E-06 major histocompatibility complex, class II, 205671_s_at HLA-DOB DO beta 3112 0.30 1.47E-06 high mobility group nucleosomal binding 202579_x_at HMGN4 domain 4 10473 0.57 7.02E-11 heterogeneous nuclear ribonucleoprotein 1554453_at HNRPLL L-like 92906 0.61 1.55E-07 interferon induced with helicase C domain 1555464_at IFIH1 1 64135 0.62 2.35E-05 201888_s_at IL13RA1 interleukin 13 receptor, alpha 1 3597 0.63 3.09E-05 205207_at IL6 interleukin 6 (interferon, beta 2) 3569 0.19 1.72E-05 227377_at IMP-1 IGF-II mRNA-binding protein 1 10642 0.18 1.52E-07 interferon stimulated gene 212766_s_at ISG20L2 20kDa-like 2 81875 0.60 1.77E-10 218170_at ISOC1 isochorismatase domain containing 1 51015 0.67 8.44E-06 212405_s_at KIAA0859 KIAA0859 51603 0.65 1.41E-07 1558293_at KIAA1107 KIAA1107 23285 0.49 5.88E-07 224927_at KIAA1949 KIAA1949 170954 0.53 1.68E-05 203333_at KIFAP3 kinesin-associated protein 3 22920 0.50 1.45E-05 lysosomal associated multispanning 201721_s_at LAPTM5 membrane protein 5 7805 0.41 4.49E-05 LATS, large tumor suppressor, homolog 2 223380_s_at LATS2 (Drosophila) 26524 0.58 4.50E-06 208885_at LCP1 lymphocyte cytosolic protein 1 (L-plastin) 3936 0.36 8.98E-05 202378_s_at LEPROT overlapping transcript 54741 0.65 4.87E-06 229349_at LIN28B lin-28 homolog B (C. elegans) 389421 0.21 4.58E-06 LOC200030 : hypothetical protein LOC200030, 242191_at LOC400781 hypothetical LOC400781 200030, 400781 0.55 1.82E-06 226901_at LOC284018 hypothetical protein LOC284018 284018 0.63 2.24E-08 hypothetical gene supported by 1568658_at LOC339804 AK075484; BC014578 339804 0.25 6.84E-06 235606_at LOC344595 hypothetical LOC344595 344595 0.41 4.06E-05 hypothetical gene supported by AL365406; 233064_at LOC388494 BC034005 388494 0.18 1.14E-07 229946_at LOC389039 similar to CDNA sequence BC043098 389039 0.66 2.86E-05 1557754_at LOC401068 hypothetical gene supported by BC028186 401068 0.47 1.33E-06 244050_at LOC401494 similar to RIKEN 4933428I03 401494 0.40 6.33E-05 LOC440667 : LOC440669 : 440667, 440669, 229872_s_at LOC440688 LOC440667, LOC440669, LOC440688 440688 0.34 1.41E-05 hypothetical gene supported by 227451_s_at LOC441130 AK026843; BX640678 441130 0.62 1.24E-06 227268_at LOC51136 PTD016 protein 51136 0.65 1.54E-05 221195_at LOC51136 PTD016 protein 51136 0.65 2.94E-05 LysM, putative peptidoglycan-binding, 232283_at LYSMD1 domain containing 1 388695 0.62 1.32E-07 myeloid cell leukemia sequence 1 (BCL2- 200797_s_at MCL1 related) 4170 0.57 1.49E-06 MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. 201930_at MCM6 cerevisiae) 4175 0.64 3.55E-06 Meis1, myeloid ecotropic viral integration 214077_x_at MEIS4 site 1 homolog 4 (mouse) 4213 0.47 3.68E-05 218897_at MGC10993 hypothetical protein MGC10993 80775 0.62 6.71E-08 similar to Six transmembrane epithelial 217553_at MGC87042 antigen of prostate 256227 0.27 7.76E-06 Page 24

202291_s_at MGP matrix Gla protein 4256 0.17 8.29E-07 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11, myeloid/lymphoid or mixed-lineage leukemia (trithorax 211071_s_at MLLT11 homolog, Drosophila); translocated to, 11 10962 0.30 1.17E-05 monocyte to macrophage differentiation- 203414_at MMD associated 23531 0.40 1.70E-07 matrix metallopeptidase 1 (interstitial 204475_at MMP1 collagenase) 4312 0.18 1.75E-05 210087_s_at MPZL1 myelin protein zero-like 1 9019 0.63 5.28E-06 208907_s_at MRPS18B mitochondrial ribosomal protein S18B 28973 0.66 3.59E-05 212944_at MRPS6 Mitochondrial ribosomal protein S6 64968 0.56 3.98E-05 MRS2-like, magnesium homeostasis factor 218538_s_at MRS2L (S. cerevisiae) 57380 0.64 5.43E-06 219451_at MSRB2 methionine sulfoxide reductase B2 22921 0.57 8.10E-05 223311_s_at MTA3 metastasis associated 1 family, member 3 57504 0.65 2.39E-07 metal response element binding 203345_s_at MTF2 transcription factor 2 22823 0.66 1.68E-09 226543_at MUTED muted homolog (mouse) 63915 0.65 1.66E-06 Neuroblastoma breakpoint family, member 227926_s_at NBPF8 20 641559 0.50 7.95E-05 NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q 201966_at NDUFS2 reductase) 4720 0.65 1.16E-05 204412_s_at NEFH , heavy polypeptide 200kDa 4744 0.15 2.24E-07 218678_at NES 10763 0.12 2.50E-08 208926_at NEU1 sialidase 1 (lysosomal sialidase) 4758 0.64 9.72E-07 202891_at NIT1 nitrilase 1 4817 0.60 3.12E-10 203964_at NMI N-myc (and STAT) interactor 9111 0.48 8.23E-07 Notch homolog 2 (Drosophila) N-terminal 227067_x_at NOTCH2NL like 388677 0.53 7.85E-09 202097_at NUP153 nucleoporin 153kDa 9972 0.59 8.70E-11 203446_s_at OCRL oculocerebrorenal syndrome of Lowe 4952 0.66 8.72E-07 pregnancy-associated plasma protein A, 224941_at PAPPA pappalysin 1 5069 0.24 6.76E-05 poly (ADP-ribose) polymerase family, 224701_at PARP14 member 14 54625 0.57 4.78E-06 Poly (ADP-ribose) polymerase family, 229264_at PARP8 member 8 79668 0.38 1.63E-05 poly (ADP-ribose) polymerase family, 223220_s_at PARP9 member 9 83666 0.63 5.78E-06 202875_s_at PBX2 pre-B-cell leukemia transcription factor 2 5089 0.67 7.35E-07 215175_at PCNX pecanex homolog (Drosophila) 22990 0.61 7.37E-05 phosphodiesterase 4D interacting protein 214130_s_at PDE4DIP (myomegalin) 9659 0.48 2.15E-07 1554789_a_at PDE8B phosphodiesterase 8B 8622 0.35 7.11E-05 218336_at PFDN2 prefoldin 2 5202 0.59 1.04E-06 204992_s_at PFN2 2 5217 0.37 7.41E-05 progesterone receptor membrane 201121_s_at PGRMC1 component 1 10857 0.59 3.04E-11 putative homeodomain transcription factor 205702_at PHTF1 1 10745 0.60 1.82E-05 202846_s_at PIGC phosphatidylinositol glycan, class C 5279 0.58 8.76E-09 phosphatidylinositol 4-kinase, catalytic, 206138_s_at PIK4CB beta polypeptide 5298 0.63 8.48E-08 phosphatidylinositol-4-phosphate 5-kinase, 207391_s_at PIP5K1A type I, alpha 8394 0.57 2.53E-05 202446_s_at PLSCR1 phospholipid scramblase 1 5359 0.66 7.73E-05 225291_at PNPT1 polyribonucleotide nucleotidyltransferase 1 87178 0.63 1.57E-06 219152_at PODXL2 podocalyxin-like 2 50512 0.41 1.54E-05 Page 25

pogo transposable element with KRAB 218229_s_at POGK domain 57645 0.66 4.97E-06 polymerase (RNA) III (DNA directed) 223269_at POLR3GL polypeptide G (32kD) like 84265 0.62 9.45E-05 protein phosphatase 1, regulatory 1566303_s_at PPP1R11 (inhibitor) subunit 11 6992 0.67 5.76E-06 protein phosphatase 2 (formerly 2A), 202883_s_at PPP2R1B regulatory subunit A (PR 65), beta isoform 5519 0.60 1.08E-06 palmitoyl-protein thioesterase 1 (ceroid- 200975_at PPT1 lipofuscinosis, neuronal 1, infantile) 5538 0.63 3.10E-09 200844_s_at PRDX6 peroxiredoxin 6 9588 0.65 2.89E-07 201858_s_at PRG1 proteoglycan 1, secretory granule 5552 0.16 4.26E-05 protein kinase, cAMP-dependent, 203680_at PRKAR2B regulatory, type II, beta 5577 0.27 3.08E-05 PRP3 pre-mRNA processing factor 3 202251_at PRPF3 homolog (yeast) 9129 0.61 1.83E-07 210988_s_at PRUNE prune homolog (Drosophila) 58497 0.59 3.02E-10 proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, proteasome (prosome, macropain) 26S subunit, non- 211609_x_at PSMD4 ATPase, 4 5710 0.67 3.32E-06 proteasome (prosome, macropain) 26S 210460_s_at PSMD4 subunit, non-ATPase, 4 5710 0.66 4.36E-06 glutaminyl-peptide cyclotransferase 205174_s_at QPCT (glutaminyl cyclase) 25797 0.12 6.91E-08 quinolinate phosphoribosyltransferase (nicotinate-nucleotide pyrophosphorylase 204044_at QPRT (carboxylating)) 23475 0.13 9.38E-06 224710_at RAB34 RAB34, member RAS oncogene family 83871 0.61 9.12E-06 222443_s_at RBM8A RNA binding motif protein 8A 9939 0.63 5.09E-10 RNA binding motif, single stranded 207266_x_at RBMS1 interacting protein 1 5937 0.65 7.56E-05 RNA binding motif, single stranded 235439_at RBMS2 interacting protein 2 5939 0.41 9.21E-05 ring finger and CCCH-type zinc finger 228996_at RC3H1 domains 1 149041 0.63 5.01E-06 209219_at RDBP RD RNA binding protein 7936 0.62 2.39E-07 RAS-like, estrogen-regulated, growth 227758_at RERG inhibitor 85004 0.19 6.47E-06 210541_s_at RFP ret finger protein 5987 0.64 3.03E-05 226433_at RNF157 ring finger protein 157 114804 0.33 3.58E-07 209111_at RNF5 ring finger protein 5 6048 0.62 1.51E-07 231131_at RP1-32F7.2 hypothetical protein FLJ37659 286499 0.08 1.11E-07 RP3- 241991_at 473B4.1 Hypothetical protein BC017868 159091 0.61 4.81E-08 ribosomal protein S6 kinase, 70kDa, 204171_at RPS6KB1 polypeptide 1 6198 0.57 6.73E-10 230378_at SCGB3A1 secretoglobin, family 3A, member 1 92304 0.31 3.30E-07 succinate dehydrogenase complex, subunit C, integral membrane protein, 215088_s_at SDHC 15kDa 6391 0.65 6.54E-08 226270_at SEC5L1 SEC5-like 1 (S. cerevisiae) 55770 0.63 2.19E-08 L (lymphocyte adhesion molecule 204563_at SELL 1) 6402 0.31 7.84E-05 serpin peptidase inhibitor, clade B 211474_s_at SERPINB6 (ovalbumin), member 6 5269 0.53 1.77E-05 203155_at SETDB1 SET domain, bifurcated 1 9869 0.61 7.43E-06 209044_x_at SF3B4 splicing factor 3b, subunit 4, 49kDa 10262 0.59 8.61E-09 213370_s_at SFMBT1 Scm-like with four mbt domains 1 51460 0.65 3.00E-06 56256_at SIDT2 SID1 transmembrane family, member 2 51092 0.66 9.78E-05 solute carrier family 19 (thiamine 209681_at SLC19A2 transporter), member 2 10560 0.53 1.04E-08 201920_at SLC20A1 solute carrier family 20 (phosphate 6574 0.56 4.16E-05 Page 26

transporter), member 1 230624_at SLC25A27 solute carrier family 25, member 27 9481 0.26 2.18E-06 231003_at SLC35B3 solute carrier family 35, member B3 51000 0.63 3.65E-05 solute carrier family 5 (sodium-dependent 204087_s_at SLC5A6 vitamin transporter), member 6 8884 0.64 2.34E-05 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 203874_s_at SMARCA1 subfamily a, member 1 6594 0.38 1.34E-05 218404_at SNX10 sorting nexin 10 29887 0.19 1.61E-07 202864_s_at SP100 nuclear antigen Sp100 6672 0.61 4.87E-06 208012_x_at SP110 SP110 nuclear body protein 3431 0.60 1.66E-05 TATA box binding protein (TBP)- associated factor, RNA polymerase I, A, 206613_s_at TAF1A 48kDa 9015 0.66 2.70E-05 208829_at TAPBP TAP binding protein (tapasin) 6892 0.54 5.75E-06 testicular cell adhesion molecule 1 233320_at TCAM1 homolog (mouse) 146771 0.24 6.65E-05 224819_at TCEAL8 transcription elongation factor A (SII)-like 8 90843 0.59 1.65E-07 209277_at TFPI2 Tissue factor pathway inhibitor 2 7980 0.13 4.96E-05 204565_at THEM2 thioesterase superfamily member 2 55856 0.59 6.23E-08 224560_at TIMP2 TIMP metallopeptidase inhibitor 2 7077 0.40 1.66E-05 231579_s_at TIMP2 TIMP metallopeptidase inhibitor 2 7077 0.40 7.23E-05 TIP41, TOR signalling pathway regulator- 1554351_a_at TIPRL like (S. cerevisiae) 261726 0.60 1.93E-08 210768_x_at TMCO1 transmembrane and coiled-coil domains 1 54499 0.51 1.59E-09 223133_at TMEM14B transmembrane protein 14B 81853 0.49 1.34E-08 219569_s_at TMEM22 transmembrane protein 22 80723 0.35 5.20E-05 1569676_at TOR1AIP2 torsin A interacting protein 2 163590 0.65 4.84E-07 203610_s_at TRIM38 tripartite motif-containing 38 10475 0.46 8.49E-05 217759_at TRIM44 tripartite motif-containing 44 54765 0.66 8.61E-09 tubulin tyrosine -like family, member 203702_s_at TTLL4 4 9654 0.62 3.53E-05 TRAF and TNF receptor associated 202266_at TTRAP protein 51567 0.60 1.15E-08 ubiquitin carboxyl-terminal 201387_s_at UCHL1 (ubiquitin thiolesterase) 7345 0.12 1.63E-05 219960_s_at UCHL5 ubiquitin carboxyl-terminal L5 51377 0.66 3.48E-06 UDP-glucose ceramide 222569_at UGCGL1 -like 1 56886 0.66 8.35E-07 235003_at UHMK1 U2AF homology motif (UHM) kinase 1 127933 0.56 7.70E-08 ubiquitin specific peptidase 32, ubiquitin 211702_s_at USP32 specific peptidase 32 84669 0.62 8.11E-07 209268_at VPS45A vacuolar protein sorting 45A (yeast) 11311 0.61 7.68E-07 202261_at VPS72 vacuolar protein sorting 72 (yeast) 6944 0.64 1.93E-05 218107_at WDR26 WD repeat domain 26 80232 0.64 9.22E-11 209196_at WDR46 WD repeat domain 46 9277 0.66 3.19E-05 219221_at ZBTB38 zinc finger and BTB domain containing 38 253461 0.65 3.75E-06 228009_x_at ZNRD1 zinc ribbon domain containing, 1 30834 0.62 6.30E-06

Page 27

Supplementary Table 6. Mutational status of TP53, EGFR, and K-ras, and response to Sagopilone

Model Response to TP53 K-ras EGFR Sagopilone Lu7298 R Y234C wt wt Lu7700 R H193Y wt wt Lu7860 R V153F wt Q787Q Lu7387 R wt wt wt Lu7668 R wt wt wt Lu7462 R G245V G12C wt Lu7336 R P190L G12D Q787Q Lu7466 R R196P wt wt Lu7506 R 190fs wt wt Lu7177 R M246V wt wt Lu7433 R E258X wt R836R Lu7064 R 162fs wt wt Lu7343 R wt wt wt Lu7414 R wt wt wt Lu7747 NR wt wt Lu7558 NR I232F wt wt Lu7166 NR wt wt wt IVS18+19; Lu7198 NR wt G12C IVS18+73 Lu7126 NR wt wt wt Lu7612 NR wt wt wt Lu7406 NR P278T wt wt Lu7187 NR wt G12C wt fs, frame shift; SD, stable disease; TP, tumor progression; TS, tumor shrinkage; wt, wild type; mutations with change in protein sequence are shaded