Published in BMC Genomics on June 09, 2014
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res (2012) 15.84
The TRANSFAC system on gene expression regulation. Nucleic Acids Res (2001) 13.63
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet (2004) 9.96
PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics (2005) 8.41
Molecular signatures database (MSigDB) 3.0. Bioinformatics (2011) 8.08
A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells. Nat Med (2006) 6.31
The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09
How to infer gene networks from expression profiles. Mol Syst Biol (2007) 5.79
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
Gene-set approach for expression pattern analysis. Brief Bioinform (2008) 4.58
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66
Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms. Oncogene (2009) 3.51
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics (2004) 3.31
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia (2007) 3.06
A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95
Wnt signaling mediates self-organization and axis formation in embryoid bodies. Cell Stem Cell (2008) 2.64
TNF-alpha/NF-kappaB/Snail pathway in cancer cell migration and invasion. Br J Cancer (2010) 2.30
ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics (2006) 2.23
A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med (2006) 2.16
Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12
ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics (2009) 2.11
SPARC and thrombospondin genes are repressed by the c-jun oncogene in rat embryo fibroblasts. EMBO J (1994) 1.25
Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol (2009) 1.15
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biol (2012) 0.95
An efficient strategy for extensive integration of diverse biological data for protein function prediction. Bioinformatics (2007) 0.95
Engineered human skin substitutes undergo large-scale genomic reprogramming and normal skin-like maturation after transplantation to athymic mice. J Invest Dermatol (2009) 0.94
Adrenomedullin promotes cell cycle transit and up-regulates cyclin D1 protein level in human glioblastoma cells through the activation of c-Jun/JNK/AP-1 signal transduction pathway. Cell Signal (2009) 0.87
Expression of thrombospondin-1 in human hepatocarcinoma cell lines and its regulation by transcription factor Jun/AP-1. Mol Cell Biochem (2001) 0.85
ADGO 2.0: interpreting microarray data and list of genes using composite annotations. Nucleic Acids Res (2011) 0.80
Adjuvant capecitabine and oxaliplatin for gastric cancer after D2 gastrectomy (CLASSIC): a phase 3 open-label, randomised controlled trial. Lancet (2012) 6.83
Collective cell guidance by cooperative intercellular forces. Nat Mater (2011) 4.64
Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet (2006) 3.76
Gabapentin receptor alpha2delta-1 is a neuronal thrombospondin receptor responsible for excitatory CNS synaptogenesis. Cell (2009) 3.46
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol (2007) 2.70
STIM1 and calmodulin interact with Orai1 to induce Ca2+-dependent inactivation of CRAC channels. Proc Natl Acad Sci U S A (2009) 2.67
Clinicopathological features and surgical treatment of gastric cancer in South Korea: the results of 2009 nationwide survey on surgically treated gastric cancer patients. J Gastric Cancer (2011) 2.59
A feed-forward loop amplifies nutritional regulation of PNPLA3. Proc Natl Acad Sci U S A (2010) 2.34
Reinforcement versus fluidization in cytoskeletal mechanoresponsiveness. PLoS One (2009) 2.22
Propulsion and navigation within the advancing monolayer sheet. Nat Mater (2013) 1.70
Identification of serum microRNAs as novel non-invasive biomarkers for early detection of gastric cancer. PLoS One (2012) 1.66
Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells. Clin Cancer Res (2005) 1.63
Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods. Helicobacter (2014) 1.59
Superior mesenteric artery syndrome: where do we stand today? J Gastrointest Surg (2012) 1.59
BWMK1, a rice mitogen-activated protein kinase, locates in the nucleus and mediates pathogenesis-related gene expression by activation of a transcription factor. Plant Physiol (2003) 1.53
Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol (2011) 1.50
Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in arabidopsis. J Biol Chem (2004) 1.47
Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1. Nucleic Acids Res (2010) 1.44
Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant Physiol (2004) 1.38
Selective binding of sterol regulatory element-binding protein isoforms and co-regulatory proteins to promoters for lipid metabolic genes in liver. J Biol Chem (2008) 1.35
Monolayer stress microscopy: limitations, artifacts, and accuracy of recovered intercellular stresses. PLoS One (2013) 1.34
Prognostic implications of and relationship between CpG island hypermethylation and repetitive DNA hypomethylation in hepatocellular carcinoma. Clin Cancer Res (2009) 1.31
TMPRSS4 induces invasion and epithelial-mesenchymal transition through upregulation of integrin alpha5 and its signaling pathways. Carcinogenesis (2010) 1.30
Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags. Int J Oncol (2006) 1.26
Collective migration and cell jamming. Differentiation (2013) 1.25
Epigenetic inactivation of protein kinase D1 in gastric cancer and its role in gastric cancer cell migration and invasion. Carcinogenesis (2008) 1.24
Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res (2006) 1.24
Defining the role of syndecan-4 in mechanotransduction using surface-modification approaches. Proc Natl Acad Sci U S A (2009) 1.22
Realization of a near-perfect antireflection coating for silicon solar energy utilization. Opt Lett (2008) 1.22
Collagen triple helix repeat containing 1 (CTHRC1) acts via ERK-dependent induction of MMP9 to promote invasion of colorectal cancer cells. Oncotarget (2014) 1.20
Epigenetic regulation of microRNA-10b and targeting of oncogenic MAPRE1 in gastric cancer. Epigenetics (2011) 1.19
Noninvasive real-time imaging of tumors and metastases using tumor-targeting light-emitting Escherichia coli. Mol Imaging Biol (2007) 1.16
Genome-wide association of serum bilirubin levels in Korean population. Hum Mol Genet (2010) 1.10
Gut bitter taste receptor signalling induces ABCB1 through a mechanism involving CCK. Biochem J (2011) 1.10
A genome-wide scan for the Sasang constitution in a Korean family suggests significant linkage at chromosomes 8q11.22-23 and 11q22.1-3. J Altern Complement Med (2009) 1.08
Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage. Hum Mol Genet (2013) 1.08
Association of serum alanine aminotransferase and γ-glutamyltransferase levels within the reference range with metabolic syndrome and nonalcoholic fatty liver disease. Korean J Hepatol (2011) 1.07
Does the CT whirl sign really predict small bowel volvulus?: Experience in an oncologic population. J Comput Assist Tomogr (2005) 1.07
Quality of life of patients with irritable bowel syndrome in Korea. Qual Life Res (2009) 1.05
Mechanosensing of substrate thickness. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 1.04
Clinicopathologic characteristics of gastric carcinoma in elderly patients: a comparison with young patients. World J Gastroenterol (2005) 1.04
ZEB2 upregulates integrin α5 expression through cooperation with Sp1 to induce invasion during epithelial-mesenchymal transition of human cancer cells. Carcinogenesis (2012) 1.03
H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res (2012) 1.02
Gene expression analysis of cultured amniotic fluid cell with Down syndrome by DNA microarray. J Korean Med Sci (2005) 1.02
MENT: methylation and expression database of normal and tumor tissues. Gene (2012) 1.01
Further evidence for involvement of a noncanonical function of uracil DNA glycosylase in class switch recombination. Proc Natl Acad Sci U S A (2009) 1.01
Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Biochem Biophys Res Commun (2006) 1.01
Elevated red cell distribution width is associated with advanced fibrosis in NAFLD. Clin Mol Hepatol (2013) 1.00
Association of a common genetic variant in prostate stem-cell antigen with gastric cancer susceptibility in a Korean population. Mol Carcinog (2011) 0.99
Quantitative analysis of cell-free DNA in the plasma of gastric cancer patients. Oncol Lett (2012) 0.98
Esophageal bezoar in a patient with achalasia: case report and literature review. Gut Liver (2010) 0.98
Role of FLASH in caspase-8-mediated activation of NF-kappaB: dominant-negative function of FLASH mutant in NF-kappaB signaling pathway. Oncogene (2005) 0.97
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering. BMC Bioinformatics (2009) 0.97
Sterol regulatory element binding protein 1a regulates hepatic fatty acid partitioning by activating acetyl coenzyme A carboxylase 2. Mol Cell Biol (2009) 0.97
Mlo, a modulator of plant defense and cell death, is a novel calmodulin-binding protein. Isolation and characterization of a rice Mlo homologue. J Biol Chem (2002) 0.97
Reactive oxygen species-mediated activation of the Akt/ASK1/p38 signaling cascade and p21(Cip1) downregulation are required for shikonin-induced apoptosis. Apoptosis (2013) 0.96
Meta- and gene set analysis of stomach cancer gene expression data. Mol Cells (2007) 0.96
Genome-wide profiling of the microRNA-mRNA regulatory network in skeletal muscle with aging. Aging (Albany NY) (2014) 0.96
Video-assisted thoracoscopic decortication for management of postpneumonic pleural empyema. Am J Surg (2004) 0.95
Methylenetetrahydrofolate reductase C677T polymorphism in patients with gastric and colorectal cancer in a Korean population. BMC Cancer (2010) 0.95
Aminolysis of 4-nitrophenyl phenyl carbonate and thionocarbonate: effects of amine nature and modification of electrophilic center from C[double bond]O to C[double bond]S on reactivity and mechanism. Org Biomol Chem (2008) 0.95
Combined hypermethylation and chromosome loss associated with inactivation of SSI-1/SOCS-1/JAB gene in human hepatocellular carcinomas. Cancer Lett (2002) 0.94
WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms. Bioinformatics (2012) 0.93
Functional polymorphism 57Val>Ile of aurora kinase A associated with increased risk of gastric cancer progression. Cancer Lett (2006) 0.93
A gene sets approach for identifying prognostic gene signatures for outcome prediction. BMC Genomics (2008) 0.93
Integrative genomics analysis reveals the multilevel dysregulation and oncogenic characteristics of TEAD4 in gastric cancer. Carcinogenesis (2013) 0.93
Epigenetic down-regulation and suppressive role of DCBLD2 in gastric cancer cell proliferation and invasion. Mol Cancer Res (2008) 0.92
Aberrant up-regulation of LAMB3 and LAMC2 by promoter demethylation in gastric cancer. Biochem Biophys Res Commun (2011) 0.92
nc886, a non-coding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer. Oncotarget (2014) 0.92
Membrane topology of helix 0 of the Epsin N-terminal homology domain. Mol Cells (2006) 0.92
The epigenetic silencing of LIMS2 in gastric cancer and its inhibitory effect on cell migration. Biochem Biophys Res Commun (2006) 0.92
Active doping of B in silicon nanostructures and development of a Si quantum dot solar cell. Nanotechnology (2011) 0.92
Frequent silencing of popeye domain-containing genes, BVES and POPDC3, is associated with promoter hypermethylation in gastric cancer. Carcinogenesis (2010) 0.92
Identification of novel genes associated with the response to 5-FU treatment in gastric cancer cell lines using a cDNA microarray. Cancer Lett (2004) 0.92
Pyruvate kinase M2 promotes the growth of gastric cancer cells via regulation of Bcl-xL expression at transcriptional level. Biochem Biophys Res Commun (2012) 0.91
An essential role of the CAAT/enhancer binding protein-alpha in the vitamin D-induced expression of the human steroid/bile acid-sulfotransferase (SULT2A1). Mol Endocrinol (2005) 0.91
Human histone H3K79 methyltransferase DOT1L protein [corrected] binds actively transcribing RNA polymerase II to regulate gene expression. J Biol Chem (2012) 0.91
SERPINE1 intron polymorphisms affecting gene expression are associated with diffuse-type gastric cancer susceptibility. Cancer (2010) 0.91
Genetic variations in the PRKAA1 and ZBTB20 genes and gastric cancer susceptibility in a Korean population. Mol Carcinog (2013) 0.91
Expression of cyclooxygenase-2, p53 and Ki-67 in gastric cancer. J Korean Med Sci (2006) 0.91
Vitamin C down-regulates VEGF production in B16F10 murine melanoma cells via the suppression of p42/44 MAPK activation. J Cell Biochem (2011) 0.90
Enhancement of antitumor effect using dendritic cells activated with natural killer cells in the presence of Toll-like receptor agonist. Exp Mol Med (2010) 0.90
AtCML8, a calmodulin-like protein, differentially activating CaM-dependent enzymes in Arabidopsis thaliana. Plant Cell Rep (2010) 0.90
Elevated fibroblast growth factor-inducible 14 expression promotes gastric cancer growth via nuclear factor-κB and is associated with poor patient outcome. Cancer Lett (2011) 0.89
Expression of survivin in gastric cancer and its relationship with tumor angiogenesis. Eur J Gastroenterol Hepatol (2006) 0.89
Common genetic variants at 1q22 and 10q23 and gastric cancer susceptibility in a Korean population. Tumour Biol (2013) 0.89
Upregulation of SPRR3 promotes colorectal tumorigenesis. Mol Med (2010) 0.89
Regulation of the dual specificity protein phosphatase, DsPTP1, through interactions with calmodulin. J Biol Chem (2003) 0.89
An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material. Exp Mol Med (2003) 0.89
Breast self-examination: defining a cohort still in need. Am J Surg (2009) 0.88
LRRC3B, encoding a leucine-rich repeat-containing protein, is a putative tumor suppressor gene in gastric cancer. Cancer Res (2008) 0.88
Sex-specific differences in the association between ABO genotype and gastric cancer risk in a Korean population. Gastric Cancer (2012) 0.88
Thyrotoxic vomiting: a case report and possible mechanisms. J Neurogastroenterol Motil (2010) 0.87
Epigenetic modification of retinoic acid-treated human embryonic stem cells. BMB Rep (2010) 0.87
Constitutive expression of mammalian nitric oxide synthase in tobacco plants triggers disease resistance to pathogens. Mol Cells (2012) 0.87
Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR. BMC Genomics (2012) 0.86
Copy number variations (CNVs) identified in Korean individuals. BMC Genomics (2008) 0.86