SUPPLEMENTARY TABLE B

EGID: Entrez Gene Identifier
SYMBOL: Gene Symbol
GENE NAME: Official Gene Name
ID: Affymetrix Probe Set
logFC: logarithmic transformation (base 2) of the fold-change between groups
AveExpr: logarithmic (base2) average expression for the group
t: moderated t-statistics
P.value: unadjusted P value
adj.P.Val: adjusted P value with the Benjamini-Hochberg method
B: B-statistics, log odds
wCLvsCLX: cell line group compared to matched secondary xenograft group


2_Differentially Expressed Genes: Probability > 0.88 and absolute FC > 2; wCLvsCLX
EGID SYMBOL GENENAME ID logFC AveExpr t P.Value adj.P.Val B
23325 KIAA1033 KIAA1033 215936_s_at 1.34 6.71 7.44 0.00 0.00 9.05
3157 HMGCS1 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) 205822_s_at 2.27 8.70 6.73 0.00 0.00 7.28
8239 USP9X ubiquitin specific peptidase 9, X-linked 230543_at 1.69 5.67 6.41 0.00 0.00 6.49
57082 CASC5 cancer susceptibility candidate 5 1552680_a_at 2.20 6.17 6.27 0.00 0.00 6.12
1004 CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 210602_s_at 3.04 4.04 6.23 0.00 0.00 6.01
25831 HECTD1 HECT domain containing 1 241683_at 1.28 4.96 6.19 0.00 0.00 5.91
83667 SESN2 sestrin 2 223195_s_at 1.77 6.78 6.06 0.00 0.00 5.59
8573 CASK calcium/calmodulin-dependent serine protein kinase (MAGUK family) 238699_s_at 1.36 6.45 5.98 0.00 0.00 5.36
2491 CENPI centromere protein I 207590_s_at 1.33 6.63 5.95 0.00 0.00 5.30
2710 GK glycerol kinase 215977_x_at 1.30 6.51 5.84 0.00 0.00 5.00
50807 DDEF1 development and differentiation enhancing factor 1 236533_at 1.53 5.63 5.78 0.00 0.00 4.84
2035 EPB41 erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked) 1554481_a_at 1.32 6.79 5.70 0.00 0.00 4.63
29005 PRO1073 PRO1073 protein 227510_x_at 2.83 7.68 5.67 0.00 0.00 4.56
2181 ACSL3 acyl-CoA synthetase long-chain family member 3 201661_s_at 1.34 8.10 5.62 0.00 0.01 4.42
5286 PIK3C2A phosphoinositide-3-kinase, class 2, alpha polypeptide 1553694_a_at 1.10 7.68 5.61 0.00 0.01 4.42
25939 SAMHD1 SAM domain and HD domain 1 1559883_s_at 1.57 5.88 5.58 0.00 0.01 4.32
57590 WDFY1 WD repeat and FYVE domain containing 1 233559_s_at 1.06 6.80 5.57 0.00 0.01 4.31
6789 STK4 serine/threonine kinase 4 205411_at 1.19 4.29 5.45 0.00 0.01 3.99
1660 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9 212107_s_at 1.65 9.35 5.29 0.00 0.01 3.57
79723 SUV39H2 suppressor of variegation 3-9 homolog 2 (Drosophila) 219262_at 1.72 4.22 5.21 0.00 0.01 3.35
114882 OSBPL8 oxysterol binding protein-like 8 228986_at 1.95 6.48 5.19 0.00 0.01 3.30
79094 CHAC1 ChaC, cation transport regulator homolog 1 (E. coli) 219270_at 1.46 5.97 5.12 0.00 0.01 3.13
4170 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 200796_s_at 1.79 6.43 5.12 0.00 0.01 3.12
340591 CA5BL carbonic anhydrase VB-like 238435_at 1.49 5.41 5.12 0.00 0.01 3.11
833 CARS cysteinyl-tRNA synthetase 240983_s_at 1.31 7.16 5.11 0.00 0.01 3.10
27125 AFF4 AF4/FMR2 family, member 4 243487_at 1.11 4.99 5.11 0.00 0.01 3.10
55055 ZWILCH Zwilch, kinetochore associated, homolog (Drosophila) 218349_s_at 1.18 8.56 5.10 0.00 0.01 3.06
6474 SHOX2 short stature homeobox 2 210134_x_at 1.33 4.80 5.09 0.00 0.01 3.03
79659 DYNC2H1 dynein, cytoplasmic 2, heavy chain 1 1561939_at 1.89 3.94 5.08 0.00 0.01 3.02
7175 TPR translocated promoter region (to activated MET oncogene) 1557227_s_at 1.97 7.01 5.08 0.00 0.01 3.01
2892 GRIA3 glutamate receptor, ionotrophic, AMPA 3 206730_at 1.06 2.72 5.08 0.00 0.01 3.00
81847 RNF146 ring finger protein 146 221430_s_at 1.28 6.58 5.08 0.00 0.01 3.00
255928 SYT14 synaptotagmin XIV 1553654_at 1.72 5.95 5.03 0.00 0.01 2.89
4800 NFYA nuclear transcription factor Y, alpha 215720_s_at 1.21 6.42 4.96 0.00 0.01 2.70
259266 ASPM asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 232238_at 1.72 6.57 4.94 0.00 0.01 2.64
2713 GK3P glycerol kinase 3 pseudogene 215966_x_at 1.10 5.45 4.91 0.00 0.01 2.56
122809 SOCS4 suppressor of cytokine signaling 4 1552792_at 1.51 5.96 4.87 0.00 0.02 2.47
4238 MFAP3 microfibrillar-associated protein 3 1552312_a_at 1.43 6.90 4.87 0.00 0.02 2.46
552889 LOC552889 hypothetical LOC552889 212113_at 1.65 8.02 4.85 0.00 0.02 2.42
23657 SLC7A11 solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 207528_s_at 1.47 4.42 4.85 0.00 0.02 2.40
54989 ZNF770 zinc finger protein 770 238687_x_at 1.05 4.47 4.83 0.00 0.02 2.35
6506 SLC1A2 solute carrier family 1 (glial high affinity glutamate transporter), member 2 1558009_at 1.66 3.21 4.81 0.00 0.02 2.31
5774 PTPN3 protein tyrosine phosphatase, non-receptor type 3 203997_at 1.27 7.12 4.81 0.00 0.02 2.29
9728 KIAA0256 KIAA0256 gene product 212451_at 1.60 6.32 4.79 0.00 0.02 2.24
481 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide 201242_s_at 2.82 9.78 4.78 0.00 0.02 2.21
6249 CLIP1 CAP-GLY domain containing linker protein 1 1558924_s_at 1.51 5.19 4.76 0.00 0.02 2.18
3308 HSPA4 heat shock 70kDa protein 4 208814_at 1.79 6.71 4.76 0.00 0.02 2.18
80267 EDEM3 ER degradation enhancer, mannosidase alpha-like 3 220342_x_at 1.34 7.14 4.75 0.00 0.02 2.14
79699 ZYG11B zyg-11 homolog B (C. elegans) 227918_s_at 2.07 6.51 4.74 0.00 0.02 2.13
55752 SEPT11 septin 11 201308_s_at 1.56 6.76 4.74 0.00 0.02 2.12
57551 TAOK1 TAO kinase 1 227454_at 1.86 7.35 4.74 0.00 0.02 2.11
10432 RBM14 RNA binding motif protein 14 1555639_a_at 1.31 7.11 4.73 0.00 0.02 2.08
9117 SEC22C SEC22 vesicle trafficking protein homolog C (S. cerevisiae) 236268_at 1.32 6.63 4.72 0.00 0.02 2.07
162494 RHBDL3 rhomboid, veinlet-like 3 (Drosophila) 233409_at -1.79 6.07 -4.73 0.00 0.02 2.09
6048 RNF5 ring finger protein 5 216018_at -1.15 4.79 -4.83 0.00 0.02 2.36
441054 LOC441054 hypothetical protein LOC441054 236915_at -1.15 4.24 -4.85 0.00 0.02 2.42
254268 C1orf62 chromosome 1 open reading frame 62 1563834_a_at -2.11 3.11 -4.87 0.00 0.02 2.46
23338 PHF15 PHD finger protein 15 212660_at -1.78 6.67 -4.88 0.00 0.02 2.47
1281 COL3A1 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 215076_s_at -3.08 6.63 -4.90 0.00 0.01 2.55
8396 PIP4K2B phosphatidylinositol-5-phosphate 4-kinase, type II, beta 1558599_at -1.22 4.01 -4.94 0.00 0.01 2.64
64772 FLJ21865 endo-beta-N-acetylglucosaminidase 220349_s_at -1.05 6.30 -5.22 0.00 0.01 3.38
509 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 214132_at -1.03 6.11 -5.36 0.00 0.01 3.75
84253 GARNL3 GTPase activating Rap/RanGAP domain-like 3 223604_at -1.49 6.10 -5.38 0.00 0.01 3.81
91368 CDKN2AIPNL CDKN2A interacting protein N-terminal like 1554348_s_at -1.26 5.07 -5.66 0.00 0.00 4.52
3039 HBA1 hemoglobin, alpha 1 214414_x_at -1.48 5.37 -5.84 0.00 0.00 5.00
4666 NACA nascent polypeptide-associated complex alpha subunit 222018_at -1.34 7.12 -6.20 0.00 0.00 5.95
7110 TMF1 TATA element modulatory factor 1 215855_s_at -1.09 5.19 -6.23 0.00 0.00 6.01
1337 COX6A1 cytochrome c oxidase subunit VIa polypeptide 1 224344_at -3.86 5.54 -10.13 0.00 0.00 15.03
3956 LGALS1 lectin, galactoside-binding, soluble, 1 (galectin 1) 216405_at -5.57 6.79 -13.86 0.00 0.00 21.43
  NA NA 217572_at -6.89 8.27 -14.02 0.00 0.00 21.66
3046 HBE1 hemoglobin, epsilon 1 217683_at -8.54 7.92 -17.71 0.00 0.00 26.18