Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis.

PubWeight™: 1.32‹?› | Rank: Top 10%

🔗 View Article (PMC 3688008)

Published in Neuro Oncol on March 15, 2013

Authors

Yong-Wan Kim1, Dimpy Koul, Se Hoon Kim, Agda Karina Lucio-Eterovic, Pablo R Freire, Jun Yao, Jing Wang, Jonas S Almeida, Ken Aldape, W K Alfred Yung

Author Affiliations

1: Cancer Research Institute of Medical Science, The Catholic University of Korea, Seoul, Korea.

Articles citing this

Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. Brief Bioinform (2014) 1.06

Beyond the World Health Organization grading of infiltrating gliomas: advances in the molecular genetics of glioma classification. Ann Transl Med (2015) 0.99

KITENIN promotes glioma invasiveness and progression, associated with the induction of EMT and stemness markers. Oncotarget (2015) 0.93

Transcriptional diversity of long-term glioblastoma survivors. Neuro Oncol (2014) 0.87

Integrated analysis of genome-wide DNA methylation, gene expression and protein expression profiles in molecular subtypes of WHO II-IV gliomas. J Exp Clin Cancer Res (2015) 0.82

CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res (2016) 0.80

Integrating multidimensional omics data for cancer outcome. Biostatistics (2016) 0.79

Chromosomal Instability and Phosphoinositide Pathway Gene Signatures in Glioblastoma Multiforme. Mol Neurobiol (2014) 0.79

Biomarkers for glioma immunotherapy: the next generation. J Neurooncol (2015) 0.78

Cancer genomic research at the crossroads: realizing the changing genetic landscape as intratumoral spatial and temporal heterogeneity becomes a confounding factor. Cancer Cell Int (2014) 0.78

Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients. Neuro Oncol (2016) 0.78

Proteomic analysis of cerebrospinal fluid: toward the identification of biomarkers for gliomas. Neurosurg Rev (2014) 0.77

Circulating tumor cell is a common property of brain glioma and promotes the monitoring system. Oncotarget (2016) 0.77

A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. BMC Syst Biol (2016) 0.76

Case comparison and literature review of glioblastoma: A tale of two tumors. Surg Neurol Int (2014) 0.75

Sample Level Enrichment Analysis of KEGG Pathways Identifies Clinically Relevant Subtypes of Glioblastoma. J Cancer (2016) 0.75

FBLN4 as candidate gene associated with long-term and short-term survival with primary glioblastoma. Onco Targets Ther (2017) 0.75

Glioblastoma - A tale of two tumors: Case comparison and literature review. Surg Neurol Int (2014) 0.75

A quantitative study of shape descriptors from glioblastoma multiforme phenotypes for predicting survival outcome. Br J Radiol (2016) 0.75

Blocking epithelial-to-mesenchymal transition in glioblastoma with a sextet of repurposed drugs: the EIS regimen. Oncotarget (2017) 0.75

PATZ1 is a new prognostic marker of glioblastoma associated with the stem-like phenotype and enriched in the proneural subtype. Oncotarget (2017) 0.75

Articles cited by this

Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09

Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics (2004) 24.18

Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell (2006) 21.66

Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits. Nat Rev Cancer (2009) 18.53

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12

The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44

Genome-wide association study identifies five susceptibility loci for glioma. Nat Genet (2009) 7.62

A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics (2003) 6.31

Analysis of gene expression data using BRB-ArrayTools. Cancer Inform (2007) 6.09

Pten and p27KIP1 cooperate in prostate cancer tumor suppression in the mouse. Nat Genet (2001) 5.92

The transcriptional repressor Snail promotes mammary tumor recurrence. Cancer Cell (2005) 5.81

Neural stem cells and the origin of gliomas. N Engl J Med (2005) 5.43

Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nat Genet (2009) 5.13

Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities. Cancer Res (2006) 4.80

Long-term survival with glioblastoma multiforme. Brain (2007) 4.51

Receptor-ligand interaction between CD44 and osteopontin (Eta-1). Science (1996) 3.84

A paradigm for class prediction using gene expression profiles. J Comput Biol (2002) 3.64

A multigene predictor of outcome in glioblastoma. Neuro Oncol (2009) 3.57

Prognostic factors for survival of patients with glioblastoma: recursive partitioning analysis. Neuro Oncol (2004) 3.25

Inactivation of p53 and Pten promotes invasive bladder cancer. Genes Dev (2009) 2.99

Gene expression profiles of serous, endometrioid, and clear cell subtypes of ovarian and endometrial cancer. Clin Cancer Res (2005) 2.72

STAT3 is required for proliferation and maintenance of multipotency in glioblastoma stem cells. Stem Cells (2009) 2.46

Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res (2009) 2.42

Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev (2009) 2.40

Influence of unrecognized molecular heterogeneity on randomized clinical trials. J Clin Oncol (2002) 2.39

The prognostic significance of phosphatidylinositol 3-kinase pathway activation in human gliomas. J Clin Oncol (2004) 2.24

Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts. Neuro Oncol (2009) 2.23

Primary glioblastomas express mesenchymal stem-like properties. Mol Cancer Res (2006) 2.18

Cancer Stem Cells and Epithelial-to-Mesenchymal Transition (EMT)-Phenotypic Cells: Are They Cousins or Twins? Cancers (Basel) (2011) 2.10

Epithelial mesenchymal transition and cancer stem cell-like phenotypes facilitate chemoresistance in recurrent ovarian cancer. Curr Cancer Drug Targets (2010) 1.91

The neurobiology of gliomas: from cell biology to the development of therapeutic approaches. Nat Rev Neurosci (2011) 1.66

Tumor necrosis factor-alpha regulates transforming growth factor-beta-dependent epithelial-mesenchymal transition by promoting hyaluronan-CD44-moesin interaction. J Biol Chem (2009) 1.56

Pten deficiency activates distinct downstream signaling pathways in a tissue-specific manner. Cancer Res (2006) 1.37

Tumor escape in a Wnt1-dependent mouse breast cancer model is enabled by p19Arf/p53 pathway lesions but not p16 Ink4a loss. J Clin Invest (2008) 1.36

A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A (2011) 1.30

Integration and analysis of genome-scale data from gliomas. Nat Rev Neurol (2011) 1.20

Exploratory analysis of the copy number alterations in glioblastoma multiforme. PLoS One (2008) 1.17

PTEN loss induces epithelial--mesenchymal transition in human colon cancer cells. Anticancer Res (2009) 1.17

Expression of transcription factor E2F1 and telomerase in glioblastomas: mechanistic linkage and prognostic significance. J Natl Cancer Inst (2005) 1.12

Cathepsin D is a potential serum marker for poor prognosis in glioma patients. Cancer Res (2005) 1.10

The PTEN phosphatase controls intestinal epithelial cell polarity and barrier function: role in colorectal cancer progression. PLoS One (2010) 1.10

Prostate epithelial Pten/TP53 loss leads to transformation of multipotential progenitors and epithelial to mesenchymal transition. Am J Pathol (2011) 1.08

Lkb1 and Pten synergise to suppress mTOR-mediated tumorigenesis and epithelial-mesenchymal transition in the mouse bladder. PLoS One (2011) 1.06

Cell- and peptide-based immunotherapeutic approaches for glioma. Trends Mol Med (2008) 1.05

Frequent mitotic errors in tumor cells of genetically micro-heterogeneous glioblastomas. Cytogenet Cell Genet (2001) 1.03

The importance of genomic copy number changes in the prognosis of glioblastoma multiforme. Neurosurg Rev (2003) 0.98

The epithelial-mesenchymal transition and the estrogen-signaling in ovarian cancer. Curr Drug Targets (2010) 0.93

Interleukin-17 stimulates the expression of IkappaB alpha mRNA and the secretion of IL-6 and IL-8 in glioblastoma cell lines. J Neuroimmunol (1999) 0.92

Clinical, histological, and immunohistochemical features predicting 1p/19q loss of heterozygosity in oligodendroglial tumors. Acta Neuropathol (2005) 0.83

Molecular pathogenesis of malignant glial tumors. Toxicol Pathol (2010) 0.82

Chromosome transfer experiments link regions on chromosome 7 to radiation resistance in human glioblastoma multiforme. Genes Chromosomes Cancer (2006) 0.79

Articles by these authors

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell (2006) 21.66

Bevacizumab alone and in combination with irinotecan in recurrent glioblastoma. J Clin Oncol (2009) 14.15

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

Molecular definition of breast tumor heterogeneity. Cancer Cell (2007) 12.67

Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet (2007) 12.62

Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature (2006) 11.90

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science (2011) 11.12

Regulation of cellular metabolism by protein lysine acetylation. Science (2010) 10.55

Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol (2008) 10.42

MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell (2007) 9.33

Effect of aciclovir on HIV-1 acquisition in herpes simplex virus 2 seropositive women and men who have sex with men: a randomised, double-blind, placebo-controlled trial. Lancet (2008) 9.17

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01

Changes in diabetes-related complications in the United States, 1990-2010. N Engl J Med (2014) 8.73

The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell (2007) 7.60

A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62

Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science (2010) 6.04

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24

Self-monitoring in weight loss: a systematic review of the literature. J Am Diet Assoc (2011) 5.12

Transforming fusions of FGFR and TACC genes in human glioblastoma. Science (2012) 5.09

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

The E3 ligase TRAF6 regulates Akt ubiquitination and activation. Science (2009) 4.63

Regulation of in situ to invasive breast carcinoma transition. Cancer Cell (2008) 4.46

Progression-free survival: an important end point in evaluating therapy for recurrent high-grade gliomas. Neuro Oncol (2008) 4.39

Distinct epigenetic changes in the stromal cells of breast cancers. Nat Genet (2005) 4.33

Priming of naive T cells inside tumors leads to eradication of established tumors. Nat Immunol (2004) 3.95

Glycolytic enzymes can modulate cellular life span. Cancer Res (2005) 3.78

Phosphatidylinositol 4 phosphate regulates targeting of clathrin adaptor AP-1 complexes to the Golgi. Cell (2003) 3.75

Large-gap quantum spin Hall insulators in tin films. Phys Rev Lett (2013) 3.60

FoxM1 promotes β-catenin nuclear localization and controls Wnt target-gene expression and glioma tumorigenesis. Cancer Cell (2011) 3.58

A multigene predictor of outcome in glioblastoma. Neuro Oncol (2009) 3.57

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet (2010) 3.56

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res (2005) 3.56

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48

Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer. Cancer Cell (2013) 3.32

TEAD transcription factors mediate the function of TAZ in cell growth and epithelial-mesenchymal transition. J Biol Chem (2009) 3.20

Sofosbuvir and Velpatasvir for HCV Genotype 2 and 3 Infection. N Engl J Med (2015) 3.13

Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Res (2005) 3.10

Skp2 targeting suppresses tumorigenesis by Arf-p53-independent cellular senescence. Nature (2010) 3.09

Epidermal growth factor receptor variant III status defines clinically distinct subtypes of glioblastoma. J Clin Oncol (2007) 3.07

HIV/STD risk behaviors and perceptions among rural-to-urban migrants in China. AIDS Educ Prev (2004) 3.04

Cell type-specific DNA methylation patterns in the human breast. Proc Natl Acad Sci U S A (2008) 2.99

Evolution of the immunoglobulin heavy chain class switch recombination mechanism. Adv Immunol (2007) 2.94

Mitochondrial Abeta: a potential focal point for neuronal metabolic dysfunction in Alzheimer's disease. FASEB J (2005) 2.91

The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet (2013) 2.89

The cholesterol absorption inhibitor ezetimibe acts by blocking the sterol-induced internalization of NPC1L1. Cell Metab (2008) 2.84

Variants in the fat mass- and obesity-associated (FTO) gene are not associated with obesity in a Chinese Han population. Diabetes (2007) 2.83

Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. J Natl Cancer Inst (2012) 2.79

Rapid cardiotonic effects of lipid emulsion infusion*. Crit Care Med (2013) 2.76

Retracted Novel HSP90 inhibitor NVP-HSP990 targets cell-cycle regulators to ablate Olig2-positive glioma tumor-initiating cells. Cancer Res (2013) 2.75

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res (2004) 2.69

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68

Trends in physical activity, sedentary behavior, diet, and BMI among US adolescents, 2001-2009. Pediatrics (2013) 2.66

Phase I trial of adenovirus-mediated p53 gene therapy for recurrent glioma: biological and clinical results. J Clin Oncol (2003) 2.63

Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock. Science (2006) 2.62

Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov (2012) 2.61

A developmental approach to complex PTSD: childhood and adult cumulative trauma as predictors of symptom complexity. J Trauma Stress (2009) 2.59

PDGF signalling controls age-dependent proliferation in pancreatic β-cells. Nature (2011) 2.53

The effect of passengers and risk-taking friends on risky driving and crashes/near crashes among novice teenagers. J Adolesc Health (2011) 2.53

Involvement of the ubiquitin-proteasome system in the early stages of wallerian degeneration. Neuron (2003) 2.51

Physics. Learning and scientific reasoning. Science (2009) 2.49

Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov (2013) 2.49

PILRalpha is a herpes simplex virus-1 entry coreceptor that associates with glycoprotein B. Cell (2008) 2.49

The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma. Genes Dev (2011) 2.48

Synaptotagmin-mediated bending of the target membrane is a critical step in Ca(2+)-regulated fusion. Cell (2009) 2.47

A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS One (2007) 2.47

Phase I/II study of imatinib mesylate for recurrent malignant gliomas: North American Brain Tumor Consortium Study 99-08. Clin Cancer Res (2006) 2.44

From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nat Biotechnol (2005) 2.41

Microarrays: retracing steps. Nat Med (2007) 2.39

NVP-BEZ235, a novel dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor, elicits multifaceted antitumor activities in human gliomas. Mol Cancer Ther (2009) 2.31

Phase II study of CCI-779 in patients with recurrent glioblastoma multiforme. Invest New Drugs (2005) 2.30

The spectrum of SCN1A-related infantile epileptic encephalopathies. Brain (2007) 2.30

Crystal structure of the clathrin adaptor protein 1 core. Proc Natl Acad Sci U S A (2004) 2.28

BMP4 supports self-renewal of embryonic stem cells by inhibiting mitogen-activated protein kinase pathways. Proc Natl Acad Sci U S A (2004) 2.25

Crash and risky driving involvement among novice adolescent drivers and their parents. Am J Public Health (2011) 2.25

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A (2012) 2.22

Growth of graphene from solid carbon sources. Nature (2010) 2.21

The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21

Enhanced striatal dopamine transmission and motor performance with LRRK2 overexpression in mice is eliminated by familial Parkinson's disease mutation G2019S. J Neurosci (2010) 2.20

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res (2006) 2.14

G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer. J Clin Invest (2012) 2.12

MSH6 mutations arise in glioblastomas during temozolomide therapy and mediate temozolomide resistance. Clin Cancer Res (2009) 2.11

Proteomic markers of DNA repair and PI3K pathway activation predict response to the PARP inhibitor BMN 673 in small cell lung cancer. Clin Cancer Res (2013) 2.09

Histopathologic characteristics of lung adenocarcinomas with epidermal growth factor receptor mutations in the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society lung adenocarcinoma classification. Arch Pathol Lab Med (2011) 2.09

Increased expression of CYP17 and CYP11B1 in subclinical Cushing's syndrome due to adrenal adenomas. Int J Urol (2011) 2.07

Disrupted autophagy leads to dopaminergic axon and dendrite degeneration and promotes presynaptic accumulation of α-synuclein and LRRK2 in the brain. J Neurosci (2012) 2.06

The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell (2009) 2.04

Applications of beta-mixture models in bioinformatics. Bioinformatics (2005) 2.04

Concordance of sustained virological response 4, 12, and 24 weeks post-treatment with sofosbuvir-containing regimens for hepatitis C virus. Hepatology (2014) 2.04

A TNF receptor family member, TROY, is a coreceptor with Nogo receptor in mediating the inhibitory activity of myelin inhibitors. Neuron (2005) 2.03

A Semantic Web management model for integrative biomedical informatics. PLoS One (2008) 2.02

Pregnancy, contraceptive use, and HIV acquisition in HPTN 039: relevance for HIV prevention trials among African women. J Acquir Immune Defic Syndr (2010) 2.01

A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics (2003) 2.01