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Supplementarytables

Table 1. Genes associated with epileptic seizures in CGGAdatabase

Gene symbol / Function of the gene / Mean RPKM value in patients with epilepsy / Mean RPKM value in patients without epilepsy / P-value
ANKRD30BP3 / Ankyrin repeat domain 30B pseudogene 3 with uncharacterized function / 0.001 / 0.011 / <0.001
LOC285627 / Uncharacterized / <0.001 / 0.006 / 0.001
CYP4F3 / This gene, CYP4F3, encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. [provided by RefSeq, Nov 2010] / 0.009 / 0.022 / 0.002
LOC100133161 / Uncharacterized / 0.042 / 0.023 / 0.002
GPR98 / GPR98, also termed Mass1 or VLGR1. The gene contains multiple calcium exchanger β or Calx-β repeats which resemble the regulatory domains of Na+/Ca2+ exchangers. A more detailed description can be found in the discussion. / 0.040 / 0.072 / 0.003
FMR1-AS1 / FMR1 antisense RNA 1. The encoded protein of FMR1 may be involved in mRNA trafficking from the nucleus to the cytoplasm. A trinucleotide repeat (CGG) in the 5' UTR is normally found at 6-53 copies, but an expansion to 55-230 repeats is the cause of fragile X syndrome. [provided by RefSeq, May 2010] / 0.006 / 0.014 / 0.003
SUV39H2 / Suppressor of variegation 3-9 homolog 2 (Drosophila) / 0.042 / 0.026 / 0.003
RINT1 / RAD50 interactor 1. It plays complex roles in the G2/M cell cycle checkpoint, maintenance of centrosome integrity, telomere elongation, Golgi apparatus, and vesicle trafficking in the endoplasmic reticulum / 6.155 / 5.365 / 0.003
CCDC62 / Coiled-coil domain containing 62, it was identified as a co-activator to enhance estrogen receptor beta-mediated transactivation and target gene expression in prostate cancer cells. / 0.094 / 0.063 / 0.004
LOC100127888 / Uncharacterized / 0.097 / 0.186 / 0.004
PCP2 / Purkinje cell protein 2 / 0.024 / 0.059 / 0.004
LPO / Lactoperoxidase, This gene encodes an oxidoreductase secreted from salivary, mammary, and other mucosal glands that functions as a natural antibacterial agent. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009] / 0.003 / <0.001 / 0.004
SOST / Loss-of-function mutations in this gene are associated with an autosomal-recessive disorder, sclerosteosis.[provided by RefSeq, Jul 2008] / 0.018 / 0.047 / 0.005
MOV10L1 / This gene is similar to a mouse gene that encodes a putative RNA helicase and shows testis-specific expression. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009] / 0.013 / 0.024 / 0.006
TRAF1 / The protein encoded by this gene is a member of the TNF receptor (TNFR) associated factor (TRAF) protein family. / 0.076 / 0.121 / 0.006
P4HA1 / This gene encodes a component of prolyl 4-hydroxylase, a key enzyme in collagen synthesis composed of two identical alpha subunits and two beta subunits. [provided by RefSeq, Jul 2008] / 0.010 / 0.021 / 0.006
UBE2D4 / Ubiquitin-conjugating enzyme E2D 4 (putative) / 8.845 / 7.576 / 0.006
RAP1B / This gene encodes a member of the RAS-like small GTP-binding protein superfamily. Members of this family regulate multiple cellular processes including cell adhesion and growth and differentiation. [provided by RefSeq, Oct 2011] / 0.040 / 0.062 / 0.006
MTRR / The protein encoded by this gene regenerates a functional methionine synthase via reductive methylation. It is a member of the ferredoxin-NADP(+) reductase (FNR) family of electron transferases. [provided by RefSeq, Jul 2008] / 0.065 / 0.090 / 0.006
PROX1 / The protein encoded by this gene is conserved across vertebrates and may play an essential role during development. Altered levels of this protein have been reported in cancers of different organs. [provided by RefSeq, Jul 2012] / 0.073 / 0.105 / 0.006
SLC52A1 / This gene encodes a member of the riboflavin (vitamin B2) transporter family. [provided by RefSeq, Jan 2013] / <0.001 / 0.002 / 0.006
SNORA77 / Small nucleolar RNA, H/ACA box 77 / 0.061 / 0.165 / 0.007
MIR210 / microRNA 210 / 0.010 / 0.067 / 0.007
BLMH / Bleomycin hydrolase (BMH) is a cytoplasmic cysteine peptidase that is highly conserved through evolution; however, the only known activity of the enzyme is metabolic inactivation of the glycopeptide bleomycin (BLM), an essential component of combination chemotherapy regimens for cancer. [provided by RefSeq, Jul 2008] / 13.066 / 11.006 / 0.007
LHB / Luteinizing hormone beta polypeptide, this gene is a member of the glycoprotein hormone beta chain family and encodes the beta subunit of luteinizing hormone (LH). Mutations in this gene are associated with hypogonadism which is characterized by infertility and pseudohermaphroditism. [provided by RefSeq, Jul 2008] / 0.055 / 0.111 / 0.007
C7orf73 / Chromosome 7 open reading frame 73 / 19.237 / 14.945 / 0.008
LPP / The encoded protein localizes to the cell periphery in focal adhesions and may be involved in cell-cell adhesion and cell motility.[provided by RefSeq, Mar 2010] / 0.004 / 0.007 / 0.008
MEGF10 / This gene encodes a member of the multiple epidermal growth factor-like domains protein family. The encoded protein plays a role in cell adhesion, motility and proliferation, and is a critical mediator of apoptotic cell phagocytosis as well as amyloid-beta peptide uptake in the brain. [provided by RefSeq, Apr 2012] / 0.033 / 0.066 / 0.008
TMLHE-AS1 / TMLHE antisense RNA 1 / 0.132 / 0.186 / 0.008
LINC00605 / Long intergenic non-protein coding RNA 605 / 0.005 / 0.018 / 0.009
UHMK1 / U2AF homology motif (UHM) kinase 1, the gene encodes a serine/threonine protein kinase that promotes cell cycle progression through G1 by phosphorylation of the cyclin-dependent kinase inhibitor 1B (p27Kip1), which causes nuclear export and degradation. The encoded protein is also thought to function in the adult nervous system and the gene has been associated with schizophrenia. [provided by RefSeq, May 2010] / <0.001 / <0.001 / 0.009
LIN7C / Lin-7 homolog C (C. elegans) / 6.653 / 5.622 / 0.009
CDKL5 / This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Mutations in this gene have been associated with X-linked infantile spasm syndrome (ISSX), also known as X-linked West syndrome, and Rett syndrome (RTT). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008] / 0.018 / 0.037 / 0.009
TRPS1 / This gene encodes a transcription factor that represses GATA-regulated genes and binds to a dynein light chain protein. Binding of the encoded protein to the dynein light chain protein affects binding to GATA consensus sequences and suppresses its transcriptional activity. Defects in this gene are a cause of tricho-rhino-phalangeal syndrome (TRPS) types I-III. [provided by RefSeq, Jul 2008] / 0.009 / 0.013 / 0.009

Table 2.Multivariate predictors of malignant progression-free survival

Characteristics / Univariable / Multivariable
P-value* / Risk ratio / 95% CI / P-value**
History of seizures / 0.713 / 0.919 / 0.196-4.313 / 0.915
Low expression of VLGR1 / 0.484 / 1.669 / 0.501-5.561 / 0.404
Age <40yrs / 0.542 / 0.526 / 0.218-2.506 / 0.627
Male / 0.685 / 1.651 / 0.465-5.862 / 0.438
Enhancementa / 0.087 / 2.823 / 0.818-9.743 / 0.101
Cortex involvement / 0.540 / 0.593 / 0.153-2.310 / 0.452

CI = confidence interval

Statistical analysis was performed using * the Kaplan-Meier log-rank test and ** the Cox proportional hazards model.

a Enhancement: Contrast enhancement on T1-weighed MR image.