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Table 1 Most characteristic genes associated with oligodendrogliomas with 1p19q codeletion

From: Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile

Probe set Title Gene Symbol Gene ontology (biological process) High expression in: FD/EGFR FD/Cx FD/CC FD/Stem cells
206785_s_at Killer cell lectin-like receptor subfamily C, member 1///member 2 KLRC1//KLRC2 Cellular defense response Natural killer cells 104.2 92.1 61.4 66.7
243779_at, 236536_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) GALNT13 Protein amino acid O-linked glycosylation Specifically expressed in neuronal cells 31.8 18.2 17.1 15.0
1558706_a_at, 228890_at Atonal homolog 8 (Drosophila) ATOH8 Regulation of transcription --- 26.1 30.8 21.4 27.1
240228_at CUB and Sushi multiple domains 3 CSMD3 Integral to membrane Brain 22.7 11.8 13.9 15.1
207723_s_at Killer cell lectin-like receptor subfamily C, member 3 KLRC3 Cellular defense response Natural killer cells 17.9 27.3 13.1 11.3
230826_at Monocyte to macrophage differentiation-associated 2 MMD2 Cytolysis --- 17.2 7.2 9.1 26.2
60474_at, 218796_at Chromosome 20 open reading frame 42 C20orf42 Cell adhesion Brain (among others) 16.2 37.4 29.1 19.6
231798_at Noggin NOG Nervous system development --- 11.2 9.2 9.5 13.6
1556599_s_at Cyclic AMP-regulated phosphoprotein, 21 kD ARPP-21 --- --- 11.1 14.0 16.8 13.9
227845_s_at Src homology 2 domain containing transforming protein D SHD Intracellular signaling cascade --- 10.3 10.6 16.5 7.6
205289_at, 205290_s_at Bone morphogenetic protein 2 BMP2 Positive regulation of astrocyte differentiation Brain (among others) 10.1 30.7 25.9 12.7
205330_at Meningioma (disrupted in balanced translocation) 1 MN1 Negative regulation of progression through cell cycle Ubiquitously expressed 8.4 5.8 9.5 15.9
219668_at Ganglioside-induced differentiation-associated protein 1-like 1 GDAP1L1 --- --- 8.4 4.2 9.1 7.9
204530_s_at Thymus high mobility group box protein TOX TOX Regulation of transcription --- 8.3 6.6 12.5 6.0
228790_at, 221959_at Chromosome 8 open reading frame 72 C8orf72 --- --- 7.6 14.6 19.1 36.6
232136_s_at Cortactin binding protein 2 CTTNBP2 --- Brain 5.4 7.1 4.3 6.5
233136_at Poly(A) binding protein, cytoplasmic 5 PABPC5 --- Fetal brain 5.4 4.6 4.6 4.9
219093_at Phosphotyrosine interaction domain containing 1 PID1 --- Brain (among others) 5.1 12.3 23.0 4.0
205773_at Cytoplasmic polyadenylation element binding protein 3 CPEB3 Nucleotide binding --- 4.5 4.0 4.8 5.4
1560265_at Glutamate receptor, ionotropic, kainate 2 GRIK2 Regulation of synaptic transmission Cerebellum, cerebral cortex 4.5 3.7 5.9 7.1
238526_at RAB3A interacting protein (rabin3) RAB3IP protein transport Brain (among others) 4.4 5.9 7.2 3.2
213001_at, 219514_at Angiopoietin-like 2 ANGPTL2 Development Heart among others 3.9 12.2 6.0 4.0
229590_at Ribosomal protein L13 RPL13 Translation --- 3.8 3.7 3.8 2.8
206117_at Tropomyosin 1 (alpha) TPM1 Cell motility Muscle among others 3.6 4.1 4.2 3.3
202315_s_at, 217223_s_at Breakpoint cluster region BCR Regulation of Rho protein signal transduction --- 3.3 4.4 7.6 4.5
234268_at Solute carrier family 2 (facilitated glucose transporter), member 13 SLC2A13 Carbohydrate transport Brain 3.1 3.4 4.1 3.2
228813_at, 204225_at Histone deacetylase 4 HDAC4 Nervous system development Ubiquitously expressed 3.1 2.6 3.9 4.4
209511_at Polymerase (RNA) II (DNA directed) polypeptide F POLR2F Regulation of transcription --- 3.0 6.9 4.7 3.0
213033_s_at, 213032_at Nuclear factor I/B NFIB Regulation of transcription, DNA-dependent, Brain development --- 3.0 10.7 13.8 8.2
204100_at Thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian) THRA Negative regulation of transcription Brain (among others) 2.9 2.9 2.2 3.7
230198_at WD repeat domain 37 WDR37 --- --- 2.8 4.0 2.8 2.6
213758_at Cytochrome c oxidase subunit IV isoform 1 COX4I1 Electron transport Ubiquitously expressed 2.4 2.2 2.7 3.2
221012_s_at Tripartite motif-containing 8///tripartite motif-containing 8 TRIM8 --- Brain (among others) 2.3 3.1 3.2 3.2
202182_at GCN5 general control of amino-acid synthesis 5-like 2 (yeast) GCN5L2 Regulation of transcription, DNA-dependent Ubiquitously expressed 2.3 2.5 2.4 2.3
214198_s_at DiGeorge syndrome critical region gene 2 DGCR2 Cell adhesion Brain (among others) 2.3 3.4 5.0 2.4
225334_at Chromosome 10 open reading frame 32 C10orf32 --- --- 2.2 3.5 4.1 3.2
210690_at Killer cell lectin-like receptor subfamily C, member 4 KLRC4 Cellular defense response Natural killer cells 2.2 2.2 2.0 2.2
203938_s_at TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa TAF1C Transcription --- 2.1 3.2 2.6 2.1
217969_at Chromosome 11 open reading frame2 C11orf2 --- --- 2.0 2.8 3.9 3.3
  1. 39 well-characterized genes were significantly upregulated (FC > 2 and p < 0.001) in oligodendrogliomas with 1p19q codeletion in comparison to each of the 4 other sample groups. Underlined genes were studied and validated by real-time RT-PCR in the independent sample set. FD/EGFR = Fold difference of geometric means (FD) in gliomas with 1p19q codeletion in comparison to gliomas with EGFR amplification, FD/Cx = FD in gliomas with 1p19q codeletion in comparison to cortex samples, FD/CC = FD in gliomas with 1p19q codeletion in comparison to corpus callosum, FD/Stem cells = FD in gliomas with 1p19q codeletion in comparison to glioblastomas cancer stem cells [7].