SUPPLEMENTARY TABLE LEGENDS:
Supplementary Table 1. Tumor samples and cell lines. Age of the patients is expressed in months. M: male; F: female. A: MYCN gene amplification; NA: euploid MYCN gene copy number. “MYCN mRNA” is the level of expression of this gene according to microarray analysis (No: expression less than 10,000 fluorescent units; Yes: more than 10,000). “MYCN protein” designates the expression of MYCN protein by immunohistochemistry and immunofluorescence assays (- no, + weak, ++ moderate, and +++ strong nuclear immunoreactivity; NA: not available, cell line protein expression data is derived from reference 25). SP: stroma poor; SR: stroma rich. TCC: tumor cell content. A: alive; D: dead.
Supplementary Table S2: Genes differentially expressed with MYCN (Kendall tau correlation and Mann-Whitney tests (P<0.01) and a mean fold-change of >3) in the analysis of all neuroblastic tumors. Functional attributes are shown for previously characterized genes. Columns labeled CACGTG and CATGTG indicate the presence of MYCN binding E-boxes sequences in the promotor region of the corresponding genes. “Affy ID” is the Affymetrix identifying number assigned to each probe set. “Transf NB CL” is the change in hybridization for each probe set consistently detected for both MYCN-transfected neuroblastoma cell lines (SK-N-ER and SK-N-AS). The column labeled “cycloh” is the change in hybridization for each probe set for MYCN-transfected SK-N-ER cell line in the presence of cycloheximide. I: increase >10%, D: decrease <10%, 0: change <10%. Fold-changes of more than 1.5 for the transfected cell lines are labeled with one asterisk (*), whereas fold-changes of more than 2 are labeled with two asterisks (**). The last column indicates whether or not each probe set was also differentially expressed in the analysis for stage 4 tumors, is indicated. “†” indicates that the gene assignment was made by BLAST search of ENSEMBL. Please, note that probe set 35158_at corresponds to a 3’ untranslated region that is not present in the pMYCN gene construct and, therefore, it is not detected after transfection.
Supplementary Table S3: Probe sets with significant Kendall tau correlation and Mann-Whitney tests (P<0.01) with a mean fold-change (FC) of 3 or more in the analysis for stage 4, stroma-poor tumors according to MYCN status. Functional attributes are shown for previously characterized genes. “Affy ID” is the identifying information assigned to each probe set. “Transf NB CL” indicates the behavior of each probe set in both MYCN-transfected neuroblastoma cell lines (SK-N-ER and SK-N-AS). “Cycloh” is the gene expression determined by the probe sets for MYCN-transfected SK-N-ER cell line in the presence of cycloheximide. I: increase of greater than 10% after pMYCN transfection, D: decrease of greater than 10% after pMYCN transfection, 0: less than 10% change. Changes of more than 50% are labeled with one asterisk (*), and more than 100% are represented with two asterisks (**). “All tumors targets” indicates whether or not each probe set was strongly differentially expressed in the analysis for all neuroblastic tumors as well. “†” indicates that the gene assignment was made by BLAST search of ENSEMBL.
Table 1:
Sample / Tumor type / Stage / SPECIMEN / Age / Sex / MYCN gene / MYCN mRNA / MYCN protein / Tissue Histology / TCC (%) / Outcome1 / NB / 3 / mediastinum / 18 / M / NA / No / - / SP / 70 / D
2 / NB / 3 / mediastinum / 10 / F / NA / No / - / SP / 90 / A
3 / NB / 3 / abdominal / 18 / M / NA / No / - / SP / 90 / A
4 / NB / 4 / adrenal / 36 / M / A / Yes / ++ / SP / 100 / A
5 / NB / 4 / adrenal / 56 / F / A / No / - / SP / 80 / D
6 / NB / 4 / adrenal / 48 / F / A / Yes / + / SP / 80 / A
7 / NB / 3 / adrenal / 36 / M / A / Yes / ++ / SP / 70 / A
8 / NB / 4N / lymph node / 204 / F / NA / No / - / SP / 80 / A
10 / NB / 4 / liver / 72 / F / NA / Yes / +++ / SP / 80 / D
11 / NB / 4 / retroperitoneal / 8 / F / NA / No / - / SP / 70 / A
12 / NB / 2 / mediastinum / 2 / F / NA / No / - / SP / 90 / A
13 / NB / 2 / cervical / 48 / F / NA / No / - / SP / 100 / A
14 / NB / 4 / adrenal / 18 / F / NA / No / - / SP / 100 / A
16 / NB / 4s / liver / 1 / M / NA / No / NA / SP / 90 / A
17 / NB / 4 / adrenal / 24 / M / A / Yes / +++ / SP / 90 / A
19 / NB / 4 / retroperitoneal / 18 / F / NA / No / - / SP / 70 / A
20 / NB / 2 / mediastinum / 24 / M / NA / No / - / SP / 90 / A
21 / NB / 4 / adrenal / 48 / F / NA / No / - / SP / 80 / A
22 / NB / 3 / adrenal / 18 / F / NA / No / - / SP / 90 / D
23 / NB / 4s / liver / 6 / M / NA / No / - / SP / 90 / A
24 / NB / 3 / retroperitoneal / 13 / F / NA / No / - / SP / 80 / A
25 / NB / 4 / liver / 6 / F / NA / No / NA / SP / 90 / A
32 / NB / 2 / retroperitoneal / 3 / F / NA / No / - / SP / 80 / A
33 / GN / GN / abdominal / 33 / F / NA / No / NA / SR / 80 / A
34 / NB / 4 / adrenal / 60 / M / NA / No / NA / MIXED SP+SR / 80 / D
35 / GN / GN / mediastinum / 63 / F / NA / No / NA / SR / 90 / A
36 / GN / GN / pelvic / adult / M / NA / No / + / SP / 80 / A
37 / NB / 2 / adrenal / 13 / M / NA / No / - / SP / 90 / A
38 / NB / 4 / adrenal / 48 / F / NA / No / - / SP+ focal SR / 80 / D
39 / NB / 4s / mediastinum / 5 / M / NA / No / - / SR / 80 / A
40 / NB / 4 / adrenal / 16 / F / A / Yes / ++ / SP / 80 / D
41 / NB / 4 / chest wall / 11 / F / NA / Yes / NA / SP / 80 / A
42 / NB / 4 / CNS / 70 / M / NA / No / - / SP / 80 / D
46 / NB / 4 / CNS / 48 / F / NA / No / - / SP / 90 / D
47 / NB / 4 / CNS / 26 / F / NA / No / NA / SP / 90 / D
53 / NB / 3 / retroperitoneal / 11 / M / NA / Yes / ++ / SP / 90 / A
54 / NB / 4 / cervical / 34 / M / A / Yes / + / SP / 80 / A
55 / NB / 3 / abdominal / 48 / F / NA / Yes / - / SP / 80 / D
56 / NB / 4 / adrenal / 16 / M / A / No / - / SP / 80 / A
57 / NB / 4 / adrenal / 6 / F / A / Yes / + / SP / 70 / A
BE (2) C / NB / CL / - / - / - / A / Yes / ++* / I / - / -
BE (2) M17 / NB / CL / - / - / - / A / Yes / ++* / N / - / -
BE (2) S / NB / CL / - / - / - / A / Yes / -* / S / - / -
LAI-55N / NB / CL / - / - / - / A / Yes / ++* / N / - / -
SH-SY5Y / NB / CL / - / - / - / NA / No / -* / N / - / -
SK-N-BE (1) N / NB / CL / - / - / - / A / Yes / ++* / N / - / -
SK-N-BE (2) N / NB / CL / - / - / - / A / Yes / ++* / N / - / -
LAI-5S / NB / CL / - / - / - / A / Yes / -* / S / - / -
SH-EP1 / NB / CL / - / - / - / NA / No / -* / S / - / -
SK-N-ER / NB / CL / - / - / - / NA / No / -* / I / - / -
SK-N-JD / NB / CL / - / - / - / A / Yes / ++* / I / - / -
SK-N-LP / NB / CL / - / - / - / A / Yes / ++* / I / - / -
60 / GN / GN / retroperitoneal / 48 / M / NA / No / - / SR / 80 / A
69 / NB / 4 / retroperitoneal / 36 / M / A / Yes / ++ / SP with fibrosis / 90 / A
72 / NB / 4 / mediastinum / 54 / M / NA / No / - / SP / 90 / A
74 / NB / 4 / adrenal / 12 / F / A / Yes / + / SP / 80 / D
77 / NB / 2 / mediastinum / 12 / M / NA / Yes / ++ / SP / 80 / D
79 / NB / 3 / retroperitoneal / 48 / F / A / Yes / ++ / SP / 90 / D
80 / NB / 4 / abdominal / 5 / M / A / Yes / + / SP / 90 / D
89 / GN / GN / mediastinum / 129 / M / NA / No / - / SR / 80 / A
* MYCN protein expression derived from reference 25
1
Supplemental Table S2:
Affy # / All tumors FC / Gene symbol / Gene name / Function / CACGTG / CATGTG / Transf. NB CL / CYCLOH / STAGE 41430_at / 0.0255 / SST† / somatostatin precursor / Apoptosis / NO / YES / 0 / 0 / NO
39631_at / 0.2196 / EMP2 / epithelial membrane protein 2 / Apoptosis / YES / NO / D / 0 / NO
59614_g_at / 11.9865 / BID / BH3 interacting domain death agonist / Apoptosis / NO / NO / 0 / 0 / NO
66141_g_at / 0.2865 / TEGT / testis enhanced gene transcript (BAX inhibitor 1) / Apoptosis / NO / YES / 0 / 0 / NO
33235_at / 0.1934 / NAV3 / neuron navigator 3 / Axon guidance / NO / YES / 0 / 0 / NO
52294_s_at / 0.1491 / NCALD / neurocalcin delta / Calcium binding protein / YES / YES / 0 / 0 / NO
33299_at / 3.0033 / CDC2L2 / cell division cycle 2-like 2 / Cell cycle regulation / NO / YES / 0 / 0 / NO
40852_at / 0.2152 / PCTAIRE2BP / tudor repeat associator with PCTAIRE 2 / Cell cycle regulation / ? / ? / 0 / 0 / NO
64405_r_at / 4.2936 / CDCA7 / cell division cycle associated 7 / Cell cycle regulation / NO / NO / 0 / 0 / YES
37323_r_at / 0.1171 / HPGD / hydroxyprostaglandin dehydrogenase 15-(NAD) / Cell metabolism / NO / YES / 0 / 0 / NO
49423_at / 0.3332 / LHPP / phospholysine phosphohistidine inorganic pyrophosphate phosphatase / Cell metabolism / NO / YES / D* / 0 / NO
1230_g_at / 0.1801 / CRA / cisplatin resistance associated / Chemotherapy resistance / NO / YES / 0 / 0 / NO
78641_at / 0.308 / EPS15 / epidermal growth factor receptor pathway substrate 15 / Control of Cell Proliferation / NO / YES / 0 / 0 / NO
34772_at / 0.2418 / CORO2B / coronin, actin binding protein, 2B / Cytoskeleton / ? / ? / 0 / D* / NO
35917_at / 0.2115 / MAP1A / microtubule-associated protein 1A / Cytoskeleton / NO / YES / 0 / 0 / YES
36591_at / 0.1503 / TUBA1 / tubulin, alpha 1 (testis specific) / Cytoskeleton / NO / YES / 0 / 0 / NO
57830_s_at / 0.1334 / HOXC10 / homeo box C10 / Development / YES / NO / 0 / 0 / NO
52922_at / 0.2639 / LR8 / LR8 protein / Development, myelin associated / NO / YES / 0 / 0 / NO
2036_s_at / 0.1814 / CD44 / CD44 antigen / Differentiation marker, adhesion / NO / YES / 0 / 0 / NO
45995_at / 4.1125 / ABCC13 / ATP-binding cassette protein C13 / Differentiation, hematopoiesis / NO / YES / 0 / 0 / NO
31751_f_at / 3.1953 / H1F5† / H4 histone family, member M / DNA associated / NO / YES / 0 / I / YES
155_s_at / 3.0068 / UBL1 / ubiquitin-like 1 (sentrin) / DNA repair / YES / YES / 0 / 0 / NO
457_s_at / 3.0754 / UBL1 / ubiquitin-like 1 (sentrin) / DNA repair / YES / YES / 0 / 0 / NO
51731_at / 9.1627 / NSE1 / non-structural maintenance of chromosomes element 1 / DNA repair / NO / YES / 0 / I / NO
37539_at / 0.2538 / RGL / RAL guanine nucleotide dissociation stimulator / DNA synthesis / NO / YES / 0 / 0 / NO
34224_at / 0.1387 / FADS3 / fatty acid desaturase 3 / Fatty acid desaturation / NO / YES / 0 / D** / NO
43394_s_at / 0.0457 / FADS3 / fatty acid desaturase 3 / Fatty acid desaturation / YES / YES / 0 / 0 / NO
49702_g_at / 0.2002 / SLC2A4RG / Glutation 4 enhancer / Glucose transport / YES / NO / 0 / 0 / NO
80389_at / 0.0171 / GRN / granulin / Growth factor / NO / YES / 0 / D / NO
41446_f_at / 0.2451 / MT1F / similar to metallothionein / Heavy metals binding / ? / ? / 0 / 0 / NO
72363_f_at / 0.0323 / IGHG1 / IG CHAIN / Immunoglobulin / NO / NO / 0 / 0 / NO
88504_at / 0.2995 / OSBPL7 / oxysterol binding protein-like 7 / Lipid receptor (intracellular) / NO / YES / 0 / 0 / NO
36958_at / 0.3307 / ZYX / zyxin / Membrane adhesion protein / YES / NO / 0 / 0 / NO
36206_at / 3.4204 / SLC16A1 / monocarboxylate transporter / Membrane protein / NO / YES / 0 / 0 / NO
424_s_at / 0.0608 / FGFR1 / fibroblast growth factor receptor 1 / Membrane protein / NO / NO / 0 / 0 / NO
57094_at / 0.262 / TMEM2 / transmembrane protein 2 / Membrane protein / NO / YES / 0 / 0 / NO
64475_at / 0.2691 / LOC83468 / hypothetical protein LOC83468 / Membrane protein / YES / YES / 0 / 0 / NO
39106_at / 0.0414 / APOA1 / apolipoprotein A-I / Metabolism / YES / YES / 0 / 0 / NO
78164_at / 4.7599 / SKRP1 / extraembryonic, spermatogenesis, homeobox 1-like / Cell signaling, development / YES / YES / 0 / 0 / NO
85089_at / 0.3022 / NUMA1 / nuclear mitotic apparatus protein 1 / Mitosis / NO / YES / 0 / D** / NO
37173_at / 3.5546 / CENPE / centromere protein E (312kD) / Mitotic spindle / YES / YES / 0 / I / NO
73096_at / 0.2437 / PMP22 / peripheral myelin protein 22 / Myelin protein / NO / YES / 0 / 0 / NO
234_s_at / 0.2889 / PTN / pleiotrophin / Nerve growth factor / NO / YES / D / 0 / NO
34820_at / 0.2942 / PTN / pleiotrophin / Nerve growth factor / NO / YES / 0 / D / NO
73233_at / 3.1388 / CASPR3 / cell recognition molecule CASPR3 / Neural differentiation / NO / NO / 0 / I / NO
35370_at / 3.1472 / STAF65(gamma) / SPTF-associated factor 65 gamma / Neural marker / NO / YES / 0 / 0 / NO
37100_at / 0.2087 / FMNL / formin-like / Neural marker / NO / YES / 0 / 0 / NO
44774_at / 0.2671 / DNER / delta-notch-like EGF repeat-containing transmembrane / Neural marker / NO / NO / 0 / D / NO
44775_g_at / 0.2621 / DNER / delta-notch-like EGF repeat-containing transmembrane / Neural marker / NO / NO / 0 / 0 / NO
64262_at / 0.304 / DNER / delta-notch-like EGF repeat-containing transmembrane / Neural marker / NO / NO / 0 / D / NO
33544_at / 3.2709 / UNC5C / unc-5 homolog B (C. elegans) / Neural receptor / NO / YES / 0 / 0 / NO
63969_f_at / 0.2769 / CLU / clusterin / Neuroendocrine granules / NO / NO / 0 / 0 / NO
46682_at / 0.0761 / GDA / guanine deaminase / Neurogenesis / YES / YES / 0 / D / NO
37286_at / 0.3054 / NRCAM / neuronal cell adhesion molecule / Neuronal marker / YES / NO / 0 / 0 / NO
45458_at / 0.0068 / ECEL1 / endothelin converting enzyme-like 1 / Neuropeptide signalling pathway / YES / NO / 0 / D / NO
41107_at / 0.1963 / SNPH / syntaphilin / Neurotransmission / NO / YES / D / D / NO
2078_s_at / 18.4692 / MYCN† / N-myc proto-oncogene / Oncogene / NO / NO / I** / I** / YES
35158_at / 25.37 / MYCN / N-myc proto-oncogene / Oncogene / NO / NO / 0 / 0 / YES
41198_at / 0.2963 / GRN / granulin / Proliferation / NO / YES / 0 / D / NO
46995_at / 0.2812 / HYPE / Huntingtin interacting protein E / Protein interactions / NO / YES / 0 / 0 / NO
41607_at / 3.4034 / OVGP1 / oviductal glycoprotein 1 / Reproduction / NO / YES / 0 / 0 / NO
53711_at / 7.572 / NOP5/NOP58 / nucleolar protein NOP5/NOP58 / Ribosome synthesis / NO / YES / I / 0 / NO
70983_s_at / 4.3394 / DBY / DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome / RNA helicase / YES / YES / 0 / I* / NO
62554_at / 10.2679 / WDR12 / WD repeat domain 12 / Signal transduction, cell cycle progression / NO / YES / 0 / 0 / NO
43041_at / 0.1923 / VAT1 / synaptic vesicle membrane protein VAT / Sinapsis / NO / NO / 0 / 0 / YES
91024_at / 0.0493 / VAT1 / synaptic vesicle membrane protein VAT / Sinapsis / NO / NO / 0 / 0 / NO
1478_at / 0.3131 / ITK / IL2-inducible T-cell kinase / T lymphocytes / YES / NO / 0 / 0 / NO
38051_at / 0.2529 / MAL / mal, T-cell differentiation protein / T lymphocytes / YES / YES / D* / 0 / NO
1841_s_at / 4.1606 / NCYM† / NCYM oncogene / Transcriptional activator / NO / YES / I / 0 / YES
35062_at / 12.5195 / NCYM / NCYM oncogene / Transcriptional activator / NO / YES / 0 / 0 / YES
38824_at / 0.288 / HTATIP2 / HIV-1 Tat interactive protein 2, 30 kDa / Transcriptional activator / YES / YES / 0 / 0 / NO
465_at / 0.3019 / HTATIP / HIV-1 Tat interactive protein, 60 kDa / Transcriptional activator / YES / YES / 0 / 0 / NO
63749_at / 0.1791 / MI-ER1 / mesoderm induction early response 1 / Transcriptional activator / ? / ? / 0 / D** / NO
37663_at / 13.3851 / DDX1 / DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 / Translational regulation / NO / YES / 0 / 0 / YES
33900_at / 0.1448 / FSTL3 / follistatin-like 3 (secreted glycoprotein) / Tumor marker / NO / NO / 0 / D* / NO
53579_at / 0.3081 / LOC118430 / small breast epithelial mucin / Tumor marker / NO / YES / D / 0 / NO
53718_at / 0.1218 / HCA112 / hepatocellular carcinoma-associated antigen 112 / Tumor marker / NO / YES / 0 / 0 / NO
35151_at / 0.3235 / DOC-1R / tumor suppressor deleted in oral cancer-related 1 / Tumor suppressor / NO / YES / 0 / 0 / NO
53472_at / 0.0692 / LGI3 / Leucine-rich glioma inactivated / Tumorigenesis / YES / YES / 0 / 0 / NO
31818_at / 0.3081 / AI024916 / unknown / Unknown / ? / ? / D / D** / NO
33501_r_at / 0.1383 / S71043 / unknown / Unknown / ? / ? / D / 0 / NO
35143_at / 38.7209 / DKFZP566A1524 / hypothetical protein DKFZp566A1524 / Unknown / NO / YES / 0 / 0 / NO
36150_at / 0.1671 / AB020649 / unknown / Unknown / ? / ? / 0 / D* / NO
38940_at / 3.0848 / AD024 / AD024 protein / Unknown / NO / YES / 0 / 0 / NO
40913_at / 0.2731 / TTR / transthyretin precursor / Unknown / YES / YES / 0 / 0 / NO
42313_at / 3.3074 / AI910858 / unknown / Unknown / YES / NO / 0 / I** / NO
43484_at / 0.1061 / AA453182 / unknown / Unknown / ? / ? / D / D / NO
44112_at / 0.2774 / LOC220058 / unknown / Unknown / ? / ? / 0 / D / NO
44577_at / 3.118 / AA029500 / unknown / Unknown / ? / ? / I / 0 / NO
44981_s_at / 0.1784 / BS4 / NEDD8 ultimate buster-1 / Unknown / ? / ? / 0 / 0 / NO
45610_at / 0.2992 / AA524743 / unknown / Unknown / NO / YES / 0 / 0 / NO
45717_at / 3.4262 / MGC13170 / hypothetical protein MGC13170 / Unknown / NO / NO / 0 / I / NO
46277_at / 0.2283 / MGC12904 / hypothetical protein MGC12904 / Unknown / YES / NO / 0 / 0 / NO
46310_at / 0.3247 / SH3BGRL3 / SH3 domain binding glutamic acid-rich protein like 3 / Unknown / YES / YES / 0 / D / NO
46659_at / 0.2467 / LOC129607 / unknown / Unknown / ? / ? / D / D / NO
47343_at / 3.8519 / AI655198 / unknown / Unknown / ? / ? / 0 / 0 / NO
47478_at / 0.2029 / LOC163706 / similar to DNB5 (deleted in neuroblastoma 5) / Unknown / ? / ? / 0 / D / NO
47698_at / 0.305 / AI821370 / unknown / Unknown / ? / ? / D / 0 / NO
48063_at / 0.3185 / AA173572 / unknown / Unknown / ? / ? / 0 / 0 / NO
48366_at / 0.3209 / AI827911 / unknown / Unknown / ? / ? / 0 / 0 / NO
48664_at / 0.1588 / AI762879 / unknown / Unknown / ? / ? / 0 / 0 / NO
48745_s_at / 0.039 / FLJ12438 / hypothetical protein FLJ12438 / Unknown / NO / NO / 0 / 0 / NO
48756_at / 0.103 / AL041728 / unknown / Unknown / ? / ? / 0 / D / NO
49514_at / 0.2071 / N25986 / unknown / Unknown / ? / ? / 0 / 0 / NO
49699_at / 4.2555 / AI693954 / unknown / Unknown / YES / YES / 0 / 0 / NO
50003_at / 0.272 / MGC4161 / hypothetical protein MGC4161 / Unknown / YES / YES / D** / D / NO
50375_at / 4.2792 / AI091460 / unknown / Unknown / YES / NO / 0 / 0 / NO
50417_at / 0.1069 / FLJ13154 / hypothetical protein FLJ13154 / Unknown / YES / YES / D / 0 / YES
50459_at / 3.4405 / AA426429 / unknown / Unknown / ? / ? / 0 / 0 / NO
50718_r_at / 0.3273 / N53480 / unknown / Unknown / ? / ? / 0 / 0 / NO
51146_at / 0.2709 / FLJ20477 / hypothetical protein FLJ20477 / Unknown / NO / NO / D** / 0 / NO
51546_at / 0.204 / AI498361 / unknown / Unknown / ? / ? / 0 / 0 / NO
51547_at / 3.4856 / AA844106 / unknown / Unknown / ? / ? / 0 / 0 / NO
51894_at / 3.9234 / R37974 / unknown / Unknown / ? / ? / 0 / 0 / NO
52163_at / 0.2057 / W23237 / unknown / Unknown / NO / YES / 0 / 0 / NO
52498_at / 0.0979 / KIAA1742 / KIAA1742 protein / Unknown / ? / ? / 0 / D / YES
52940_at / 0.1044 / AA085764 / unknown / Unknown / ? / ? / 0 / 0 / NO
53849_at / 3.2172 / AI298324 / unknown / Unknown / NO / YES / 0 / 0 / NO
53941_i_at / 4.3269 / AI292214 / unknown / Unknown / ? / ? / 0 / I** / NO
54099_at / 6.5543 / AA974610 / unknown / Unknown / NO / YES / 0 / 0 / NO
55019_at / 0.2786 / FLJ21610 / hypothetical protein FLJ21610 / Unknown / NO / NO / 0 / 0 / YES
55484_r_at / 0.0963 / R54660 / unknown / Unknown / YES / NO / 0 / 0 / NO
55590_at / 0.3181 / AI652861 / unknown / Unknown / ? / ? / 0 / D / NO
55741_at / 0.2966 / AI655888 / unknown / Unknown / ? / ? / D** / 0 / NO
55923_at / 0.2881 / AA630626 / unknown / Unknown / ? / ? / D** / D* / NO
56133_at / 0.1593 / AI971535 / unknown / Unknown / ? / ? / 0 / D / YES
56455_at / 3.5125 / AA659061 / unknown / Unknown / NO / YES / 0 / 0 / NO
56814_at / 0.2607 / AA835008 / unknown / Unknown / ? / ? / 0 / 0 / NO
56836_at / 0.2112 / AW007189 / unknown / Unknown / ? / ? / 0 / 0 / NO
57226_at / 0.1315 / FLJ22174 / hypothetical protein FLJ22174 / Unknown / YES / NO / 0 / D** / NO
57528_at / 0.2434 / AI824037 / unknown / Unknown / ? / ? / 0 / 0 / NO
57585_at / 5.0522 / AI202201 / unknown / Unknown / ? / ? / 0 / 0 / NO
57600_at / 7.4449 / R38692 / unknown / Unknown / ? / ? / 0 / I** / YES
58328_at / 3.7244 / LOC164971 / hypothetical protein LOC164971 / Unknown / NO / NO / 0 / I** / NO
58756_at / 12.2867 / AA922936 / unknown / Unknown / ? / ? / 0 / 0 / YES
59070_at / 0.0869 / AI458306 / unknown / Unknown / NO / NO / 0 / 0 / NO
59717_at / 0.1439 / AA393673 / unknown / Unknown / ? / ? / 0 / D / NO
60246_at / 0.2348 / LOC129607 / hypothetical protein LOC129607 / Unknown / ? / ? / 0 / 0 / NO
60849_at / 0.1318 / C20orf103 / chromosome 20 open reading frame 103 / Unknown / NO / YES / 0 / D / NO
60887_s_at / 0.2944 / LOC253980 / hypothetical protein LOC253980 / Unknown / ? / ? / 0 / D** / NO
61011_at / 6.4457 / AI203206 / unknown / Unknown / ? / ? / 0 / I** / NO
61384_r_at / 0.2452 / AA393134 / unknown / Unknown / ? / ? / 0 / 0 / NO
61638_at / 0.1915 / DKFZP761E1824 / hypothetical protein DKFZp761E1824 / Unknown / ? / ? / 0 / 0 / NO
62214_at / 0.2515 / LGP2 / likely ortholog of mouse D11lgp2 / Unknown / YES / NO / 0 / D* / NO
64419_at / 11.6249 / DKFZP566A1524 / hypothetical protein DKFZp566A1524 / Unknown / NO / YES / 0 / 0 / YES
64610_at / 0.327 / N59432 / unknown / Unknown / YES / NO / 0 / D** / NO
64707_r_at / 0.0931 / AI968291 / unknown / Unknown / ? / ? / 0 / 0 / NO
65846_at / 0.1763 / AI268230 / unknown / Unknown / NO / YES / 0 / 0 / NO
65891_at / 3.5663 / TH1L / TH1-like (Drosophila) / Unknown / NO / YES / I / I** / NO
66261_at / 0.2246 / AI792080 / unknown / Unknown / NO / NO / 0 / D** / NO
66759_at / 3.7455 / AA971264 / unknown / Unknown / ? / ? / 0 / I** / NO
66835_at / 0.1503 / AA988736 / unknown / Unknown / ? / ? / 0 / 0 / NO
67031_at / 0.2048 / AA931376 / unknown / Unknown / ? / ? / 0 / 0 / NO
67101_at / 11.9532 / AI347542 / unknown / Unknown / ? / ? / 0 / 0 / NO
67493_at / 0.0924 / AI912887 / unknown / Unknown / NO / YES / 0 / 0 / NO
68169_r_at / 0.2899 / MGC4840 / hypothetical protein MGC4840 / Unknown / ? / ? / 0 / D** / NO
68272_at / 4.1245 / AA702795 / unknown / Unknown / ? / ? / 0 / I* / NO
68284_at / 4.0224 / AA781101 / unknown / Unknown / ? / ? / 0 / 0 / NO
68892_at / 4.0808 / AI468307 / unknown / Unknown / NO / NO / 0 / 0 / NO
69093_at / 3.178 / AI025501 / unknown / Unknown / ? / ? / 0 / 0 / NO
69605_at / 0.1643 / AI741993 / unknown / Unknown / ? / ? / D / D / NO
70093_at / 0.2777 / AI806727 / unknown / Unknown / YES / YES / 0 / D* / NO
70290_at / 5.0094 / AI808609 / unknown / Unknown / ? / ? / 0 / 0 / NO
70741_at / 4.2578 / AA404996 / unknown / Unknown / NO / YES / 0 / 0 / NO
71119_at / 0.3237 / AI919163 / unknown / Unknown / NO / YES / 0 / D / NO
71283_at / 0.2169 / R35259 / unknown / Unknown / YES / NO / 0 / 0 / NO
71616_r_at / 0.2075 / R27430 / unknown / Unknown / ? / ? / 0 / 0 / NO
72041_at / 3.5413 / AI219911 / unknown / Unknown / NO / NO / 0 / 0 / NO
72120_at / 4.9957 / AA513644 / unknown / Unknown / ? / ? / 0 / I** / NO
72540_r_at / 0.3241 / AI187767 / unknown / Unknown / ? / ? / 0 / 0 / NO
72805_at / 0.2874 / AI656325 / unknown / Unknown / YES / YES / 0 / 0 / NO
73044_s_at / 0.164 / AA628795 / unknown / Unknown / ? / ? / 0 / 0 / NO
73050_at / 0.1897 / AI818514 / unknown / Unknown / NO / YES / 0 / D** / NO
73470_at / 8.7494 / AA483648 / unknown / Unknown / NO / NO / 0 / 0 / NO
73842_at / 0.1459 / ZDHHC12 / zinc finger, DHHC domain containing 12 / Unknown / NO / YES / 0 / 0 / NO
73933_at / 20.1254 / AI934342 / unknown / Unknown / ? / ? / 0 / 0 / NO
74229_at / 0.3266 / FLJ12649 / hypothetical protein FLJ12649 / Unknown / YES / YES / D* / D** / NO
74541_at / 0.1798 / AI969879 / unknown / Unknown / ? / ? / 0 / D* / NO
74941_s_at / 0.0504 / LOC221002 / hypothetical protein LOC221002 / Unknown / NO / YES / D* / 0 / NO
75012_at / 0.0395 / AI989698 / unknown / Unknown / YES / YES / 0 / 0 / NO
75382_i_at / 0.1155 / AI382415 / unknown / Unknown / NO / NO / 0 / 0 / NO
75646_at / 0.127 / H93027 / unknown / Unknown / ? / ? / 0 / 0 / NO
76658_at / 0.1963 / ZNF237 / zinc finger protein 237 / Unknown / NO / YES / D / D** / NO
76768_at / 0.0984 / AI792267 / unknown / Unknown / ? / ? / 0 / D / NO
76769_at / 0.0843 / AI758223 / unknown / Unknown / ? / ? / 0 / 0 / NO
77466_r_at / 4.9022 / FLJ11184 / hypothetical protein FLJ11184 / Unknown / NO / YES / 0 / I* / NO
77497_s_at / 0.2432 / AI655320 / unknown / Unknown / ? / ? / 0 / 0 / YES
78075_at / 6.3385 / AI022411 / unknown / Unknown / ? / ? / I** / 0 / NO
78589_at / 0.2596 / AI190616 / unknown / Unknown / ? / ? / 0 / D / YES
78731_at / 0.3091 / N21030 / unknown / Unknown / ? / ? / 0 / 0 / NO
78882_at / 0.0858 / AA972965 / unknown / Unknown / ? / ? / D / D** / NO
79433_at / 0.0807 / AA628343 / unknown / Unknown / ? / ? / 0 / 0 / YES
80350_at / 4.126 / AI571306 / unknown / Unknown / NO / YES / 0 / 0 / NO
80491_at / 0.1267 / AI373223 / unknown / Unknown / ? / ? / 0 / D* / NO
81039_at / 0.2226 / AI797063 / unknown / Unknown / ? / ? / 0 / D** / NO
81389_at / 0.0737 / AA652566 / unknown / Unknown / ? / ? / 0 / D / NO
81520_at / 76.1968 / NAG / neuroblastoma-amplified protein / Unknown / NO / YES / 0 / I* / YES
81589_at / 0.2789 / H41870 / unknown / Unknown / ? / ? / 0 / 0 / NO
81946_at / 5.1696 / AI939458 / unknown / Unknown / NO / NO / 0 / 0 / NO
82067_at / 3.1636 / AI480300 / unknown / Unknown / YES / YES / 0 / I / NO
82680_at / 0.2613 / AL038860 / unknown / Unknown / ? / ? / 0 / 0 / YES
82733_at / 14.8274 / RAB20 / member RAS oncogene family / Unknown / NO / NO / 0 / I / NO
83496_at / 0.0394 / AI337390 / unknown / Unknown / NO / YES / 0 / 0 / NO
84014_at / 12.49 / AI039941 / unknown / Unknown / NO / YES / 0 / 0 / NO
84050_at / 0.0535 / AI583750 / unknown / Unknown / ? / ? / 0 / 0 / NO
85019_at / 10.6791 / F02458 / unknown / Unknown / NO / YES / 0 / 0 / NO
85341_at / 3.415 / AI498957 / unknown / Unknown / ? / ? / 0 / 0 / NO
85385_at / 0.1187 / T73730 / unknown / Unknown / NO / YES / 0 / 0 / NO
85874_at / 4.9097 / FLJ20171 / hypothetical protein FLJ20171 / Unknown / NO / YES / 0 / 0 / NO
86351_at / 0.2362 / HT008 / uncharacterized hypothalamus protein HT008 / Unknown / NO / YES / 0 / D / NO
86618_at / 11.6077 / AA779279 / unknown / Unknown / YES / YES / 0 / 0 / NO
86971_at / 3.2009 / AI819352 / unknown / Unknown / NO / NO / 0 / 0 / NO
87419_r_at / 3.9598 / AI679413 / unknown / Unknown / NO / NO / 0 / 0 / NO
88722_at / 3.3011 / AI669469 / unknown / Unknown / ? / ? / 0 / I* / NO
88939_at / 0.2002 / AI934452 / unknown / Unknown / YES / YES / D** / 0 / NO
88998_at / 7.2408 / AI798407 / unknown / Unknown / NO / YES / 0 / I** / NO
89092_r_at / 3.2874 / AI792841 / unknown / Unknown / ? / ? / I / I** / NO
90236_at / 0.1963 / AI692302 / unknown / Unknown / ? / ? / 0 / 0 / NO
90400_at / 0.0605 / AI027294 / unknown / Unknown / ? / ? / 0 / 0 / NO
90603_at / 0.0589 / AI916544 / unknown / Unknown / ? / ? / 0 / D** / NO
91742_at / 0.2923 / LOC127262 / hypothetical protein LOC127262 / Unknown / ? / ? / 0 / 0 / NO
57162_at / 0.0288 / ARF1GAP / ADP ribosylation factor 1 GTPase activating / Vesicle formation and coating / NO / YES / 0 / D / YES
Supplemental Table S3:
Affy ID / Stage 4 FC / Gene / Name / Function / Transf. NB CL / Cycloh. / All tumors target82590_at / 0,11641444 /
BCL2L1
/ BCL2-like 1 / Apoptosis inhibitor / 0 / 0 / NO32089_at / 0,2492164 / SPAG6 / Sperm associated antigen 6 / Axoneme / D / 0 / NO
38524_at / 0,25000691 / OCLN / Occludin / Cell adhesion / 0 / 0 / NO
82309_at / 0,32784202 / PCDHB4 / Protocadherin beta 4 / Cell adhesion; Neurogenesis / D** / 0 / NO
64405_r_at / 3,50392304 / CDCA7 / cell division cycle associated 7 / Cell cycle regulation / 0 / 0 / YES
79917_at / 4,2366875 / LOC166867† / Similar to tre-2/USP6, BUB2, cdc16 domain family, member 1 / Cell cycle regulation / 0 / 0 / NO
36996_at / 0,31062921 / OS-9 / Amplified in osteosarcoma / Cell growth and maintenance / 0 / 0 / NO
34288_at / 3,521625 / RDC1 / G protein-coupled receptor / Chemokine receptor / 0 / I* / NO
49412_at / 0,28238698 / FGF9 / fibroblast growth factor 9 (glia-activating factor) / Control of neural cell proliferation / 0 / 0 / NO
35081_at / 0,29105239 / FGF9 / fibroblast growth factor 9 (glia-activating factor) / Control of neural cell proliferation / D / D** / NO
48151_at / 3,92592348 / DNCH1 / dynein, cytoplasmic, heavy polypeptide 1 / Cytoskeleton / 0 / 0 / NO
35917_at / 0,3333221 / MAP1A / microtubule-associated protein 1A / Cytoskeleton / 0 / 0 / YES
293_at / 0,23655935 / Hpx-42 / Homeotic Protein Hpx-42 / Development / 0 / D** / NO
31751_f_at / 3,02075 / H1F5† / H4 histone family, member M / DNA associated / 0 / I / YES
90984_at / 3,89918649 / CHD1L / Chromodomain helicase DNA binding protein / DNA-binding protein / 0 / I / NO
670_s_at / 4,98161409 / CRE-Bpa / cAMP response element-binding protein CRE-Bpa / DNA-binding protein / I / I* / NO
83680_at / 5,5974375 / NR5A1 / Nuclear receptor subfamily 5, group A, member 1 / DNA-binding protein / 0 / 0 / NO
44160_at / 0,19301886 / VPS33A / Similar to rat vacuolar sorting protein 33a / Golgi-to-lysosome trafficking / 0 / D** / NO
32364_at / 0,20948358 / SIX6 / Sine oculis homeobox homolog 6 (Drosophila / Histogenesis and organogenesis / D / 0 / NO
76073_at / 5,964875 / HPGD / Hydroxyprostaglandin dehydrogenase 15-(NAD) / Inactivation of prostaglandins / 0 / 0 / NO
74846_f_at / 0,32841138 / C3F / Putative protein similar to nessy (Drosophila) / Membrane protein / 0 / 0 / NO
73253_at / 3,07031989 / SLC16A1 / Solute carrier family 16, member 1 / Membrane transporter / 0 / I** / NO
40236_at / 0,2886836 / SLC7A2 / Solute carrier family, member 2 / Membrane transporter / D** / 0 / NO
35592_at / 0,11370246 / SLC8A2 / Solute carrier family 8, member 2 / Membrane transporter / 0 / 0 / NO
40183_at / 0,21779581 / CARM1 / Coactivator-associated arginine methyltransferase 1 / Myogenesis / D / 0 / NO
78382_r_at / 3,2079375 / DISC1 / Disrupted in schizophrenia 1 / Neural protein / 0 / 0 / NO
90771_s_at / 7,6529375 / NUP153 / Nucleoporin 153kD / Nuclear transport factor / 0 / I** / NO
1277_at / 0,15378518 / ARHGEF16 / Rho guanine exchange factor (GEF) 16 / Nucleic acid metabolism / D* / D / NO
76913_at / 3,93275 / ATIC / 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase / Nucleic acid metabolism / 0 / 0 / NO
38852_at / 0,09368019 / CENTG1 / Centaurin, gamma 1 / Nucleic acid metabolism / D** / 0 / NO
63267_at / 0,1242236 / RENT2 / Regulator of nonsense transcripts 2 / Nucleoside transporter / 0 / D** / NO
1888_s_at / 3,187875 / KIT / v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog / Oncogene / 0 / 0 / NO
35158_at / 17,39722 / MYCN / N-myc proto-oncogene / Oncogene / 0 / 0 / YES
2078_s_at / 13,6406506 / MYCN† / N-myc proto-oncogene / Oncogene / I** / I** / YES
43683_at / 9,0560625 / TGFBI / Transforming growth factor, beta-induced, 68kD / Oncogenesis? / 0 / 0 / NO
91371_at / 5,0126875 / DIAPH2 / Diaphanous 2 isoform 12C / Oogenesis? / 0 / I / NO
33709_at / 0,31310591 / PDE9A / Phosphodiesterase 9A / Signal transduction / 0 / 0 / NO
43041_at / 0,30505882 / VAT1 / synaptic vesicle membrane protein VAT / Sinapsis / D / D / YES
35062_at / 9,9426875 / NCYM / NCYM oncogene / Transcriptional activator / 0 / 0 / YES
1841_s_at / 3,49097524 / NCYM† / NCYM oncogene / Transcriptional activator / I / 0 / YES
37663_at / 14,0247942 / DDX1 / DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 / Translational regulation / 0 / 0 / YES
32610_at / 4,72379359 / RIL / LIM domain protein / tumor suppressor / 0 / 0 / NO
55733_at / 0,25372783 / AA504781 / unknown / Unknown / D* / D** / NO
79433_at / 0,07104272 / AA628343 / unknown / Unknown / 0 / 0 / YES
76055_at / 4,75223918 / AA707217 / unknown / Unknown / I / 0 / NO
58615_s_at / 6,6495 / AA878237 / unknown / Unknown / 0 / 0 / NO
47296_at / 3,6360625 / AA906074 / unknown / Unknown / 0 / 0 / NO
58756_at / 6,5894375 / AA922936 / unknown / Unknown / I / 0 / YES
78589_at / 0,19076828 / AI190616 / unknown / Unknown / 0 / D* / YES
55048_at / 0,16056102 / AI221251 / unknown / Unknown / 0 / 0 / NO
52728_at / 0,28859388 / AI271605 / unknown / Unknown / 0 / D** / NO
84693_at / 13,6188215 / AI435129 / unknown / Unknown / 0 / 0 / NO
88196_at / 0,10749488 / AI480292 / unknown / Unknown / 0 / D* / NO
44396_at / 0,20322184 / AI492412 / unknown / Unknown / D** / D / NO
91557_at / 12,4075 / AI498602 / unknown / Unknown / 0 / 0 / NO
77497_s_at / 0,19542701 / AI655320 / unknown / Unknown / 0 / 0 / YES
89299_at / 0,31580226 / AI762877 / unknown / Unknown / 0 / D / NO
47916_at / 0,14939076 / AI796794 / unknown / Unknown / D / 0 / NO
62033_at / 3,099625 / AI803583 / unknown / Unknown / I** / 0 / NO
79273_r_at / 0,25672926 / AI884422 / unknown / Unknown / D** / D* / NO
76081_at / 4,713 / AI887642 / unknown / Unknown / 0 / I* / NO
47134_at / 4,6425 / AI935766 / unknown / Unknown / 0 / I** / NO
56133_at / 0,19258768 / AI971535 / unknown / Unknown / 0 / D / YES
82680_at / 0,26996804 / AL038860 / unknown / Unknown / 0 / 0 / YES
75354_at / 0,12059497 / AW000980 / unknown / Unknown / 0 / D / NO
64419_at / 10,8128085 / DKFZP566A1524 / hypothetical protein DKFZp566A1524 / Unknown / 0 / 0 / YES
66768_at / 0,22430809 / FLJ12735 / hypothetical protein FLJ12735 / Unknown / 0 / 0 / NO
50417_at / 0,24623797 / FLJ13154 / hypothetical protein FLJ13154 / Unknown / D / 0 / YES
65624_at / 0,21845435 / FLJ20037 / hypothetical protein FLJ20037 / Unknown / 0 / 0 / NO
55019_at / 0,2757041 / FLJ21610 / hypothetical protein FLJ21610 / Unknown / 0 / D / YES
84273_at / 3,20131709 / FLJ22624 / hypothetical protein FLJ22624 / Unknown / 0 / I** / NO
78556_at / 0,1043921 / H16441 / unknown / Unknown / 0 / 0 / NO
32371_at / 3,6598125 / KIAA0527 / KIAA0527 protein / Unknown / 0 / I* / NO
52498_at / 0,1889174 / KIAA1742 / KIAA1742 protein / Unknown / 0 / D / YES
46876_at / 4,772375 / N67159 / unknown / Unknown / 0 / I** / NO
81520_at / 82,2072579 / NAG / neuroblastoma-amplified protein / Unknown / 0 / I** / YES
57600_at / 8,63283607 / R38692 / unknown / Unknown / 0 / I** / YES
31738_at / 0,31034032 / W28912 / unknown / Unknown / D* / 0 / NO
57162_at / 0,0674903 / ARF1GAP / ADP ribosylation factor 1 GTPase activating / Vesicle formation and coating / 0 / D / YES
1