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

BMC Cancer

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)

	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

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.
^*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.
^#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.
^§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.
^¶Likely overbalanced gene expression as chromosome Y-linked gene (see Table 1).

ISSN: 1471-2407