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Table 2 Probe sets ID, with relative mRNA Accession or Ensembl Transcript ID, gene symbols of genes regulated in the comparison between cultures of human GBM tumorigenic cells with the highly diffusive (HD-type) and the nodular-like (NL-type) invasive patterns, as determined by using SAM software with two-class unpaired analysis and the additional requirement of at least a 2-fold change in gene expression (Ratio)

From: Identification of a novel set of genes reflecting different in vivo invasive patterns of human GBM cells

  Probe Set ID mRNA Accession / ENSEMBL transcript ID Gene Symbol Ratio HD / NL expression q-value (%)*
1 8098021 NM_001083619 GRIA2 12.92 4.76
2 8144917 NM_000237 LPL 12.41 7.14
3 8151525 NM_002677 PMP2 10.90 4.76
4 7933672 NM_033056 PCDH15 10.68 4.17
5 7906205 NM_021948 BCAN 10.39 4.17
6 8168517 NM_005296 LPAR4 8.11 6.25
7 8097449 NM_032961 PCDH10 7.97 27.32
8 8107722 NM_032446 MEGF10 6.53 13.83
9 8135705 NM_012281 KCND2 6.36 22.98
10 8103736 NM_007281 SCRG1 6.14 0.00
11 8110932 NM_003966 SEMA5A 5.59 19.23
12 8065071 NM_198391 FLRT3 5.55 0.00
13 8146403 NM_018967 SNTG1 5.48 29.51
14 7954899 NM_001843 CNTN1 5.37 25.00
15 8055496 NM_018557 LRP1B 4.99 4.76
16 8095303 NM_015236 LPHN3 4.90 31.71
17 7947553 NM_020929 LRRC4C 4.83 5.56
18 8150978 NM_004056 CA8 4.60 0.00
19 8056457 NM_006920 SCN1A 4.51 3.70
20 8112881 ENST00000388321 --- 4.48 29.51
21 8170307 NM_032539 SLITRK2 4.19 4.76
22 8162940 NM_005502 ABCA1 4.02 19.39
23 8082846 NM_004441 EPHB1 3.90 10.98
24 8037363 NM_145296 CADM4 3.88 25.17
25 7980580 NM_000153 GALC 3.57 25.00
26 7908812 NM_004767 GPR37L1 3.43 13.04
27 7970831 NM_007106 UBL3 3.22 10.98
28 8024712 NM_033064 ATCAY 2.98 4.17
29 8004081 NM_153018 ZFP3 2.96 4.76
30 8124280 NM_015864 C6orf32 0.36 3.57
31 7962579 BC095477 AMIGO2 0.29 3.45
32 8176375 NM_001008 RPS4Y1 0.21 20.80
33 8120719 NM_133493 CD109 0.18 20.72
34 8176719 NM_004681 EIF1AY 0.08 0.00
  1. The false discovery rates are expressed as q-values1. Genes with GO term “cell adhesion”# are shown in bold whereas genes with GO term “intrinsic to membrane”§ are shown with a gray background. A short description of the known functions of these genes and their full names as reported by http://www.genecards.org, are shown in the Additional File 5.
  2. *The “q-value” is for each gene, the lowest False Discovery Rate at which that gene is called significant. It is like the well-known p-value, but adapted to multiple-testing situations.
  3. #Gene Ontology cell adhesion definition: the attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
  4. §Gene Ontology intrinsic to membrane definition: located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane.
  5. Likely overbalanced gene expression as chromosome Y-linked gene (see Table 1).
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BMC Cancer

ISSN: 1471-2407

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