Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma.

PubWeight™: 0.92‹?›

🔗 View Article (PMC 3535701)

Published in BMC Genomics on December 17, 2012

Authors

Lingyao Zeng1, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li, Lu Xie

Author Affiliations

1: School of Life Science and Technology, Tongji University, Shanghai 200092, PR China.

Articles citing this

Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics (2012) 1.01

Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma. BMC Genomics (2014) 0.90

MiR-30a-5p suppresses cell growth and enhances apoptosis of hepatocellular carcinoma cells via targeting AEG-1. Int J Clin Exp Pathol (2015) 0.82

MicroRNAs associated with HBV infection and HBV-related HCC. Theranostics (2014) 0.81

Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis. Am J Cancer Res (2015) 0.78

Identifying prognostic features by bottom-up approach and correlating to drug repositioning. PLoS One (2015) 0.77

Circulating MicroRNAs in Plasma of Hepatitis B e Antigen Positive Children Reveal Liver-Specific Target Genes. Int J Hepatol (2014) 0.77

MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations. Biomark Insights (2016) 0.77

Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation. Sci China Life Sci (2014) 0.77

Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PLoS One (2014) 0.76

Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework. BMC Bioinformatics (2014) 0.75

Biological Networks for Cancer Candidate Biomarkers Discovery. Cancer Inform (2016) 0.75

MicroRNA-204-5p inhibits invasion and metastasis of laryngeal squamous cell carcinoma by suppressing forkhead box C1. J Cancer (2017) 0.75

Promising significance of the association of miR-204-5p expression with clinicopathological features of hepatocellular carcinoma. Medicine (Baltimore) (2017) 0.75

Articles cited by this

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61

Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell (2005) 14.57

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49

Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18

A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med (2007) 10.47

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46

A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19

Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput (2000) 8.02

MicroRNAs and cancer: short RNAs go a long way. Cell (2009) 7.25

miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA (2008) 5.48

Requirement for phosphatidylinositol-3 kinase in the prevention of apoptosis by nerve growth factor. Science (1995) 4.23

Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19

MicroRNA-204 regulates Runx2 protein expression and mesenchymal progenitor cell differentiation. Stem Cells (2010) 3.16

Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma. Gastroenterology (2011) 2.66

Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci U S A (2001) 2.66

Information-theoretic inference of large transcriptional regulatory networks. EURASIP J Bioinform Syst Biol (2007) 2.65

Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun (2010) 2.54

GlobalANCOVA: exploration and assessment of gene group effects. Bioinformatics (2007) 2.24

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol (2010) 1.92

miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res (2009) 1.78

The role of Notch signaling pathway in epithelial-mesenchymal transition (EMT) during development and tumor aggressiveness. Curr Drug Targets (2010) 1.75

Recursive partitioning as an approach to selection of immune markers for tumor diagnosis. Clin Cancer Res (2003) 1.72

The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays (2009) 1.72

microRNA-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma. Mol Syst Biol (2010) 1.69

MicroRNA-30a inhibits epithelial-to-mesenchymal transition by targeting Snai1 and is downregulated in non-small cell lung cancer. Int J Cancer (2011) 1.58

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics (2009) 1.45

Cross-talk between miRNA and Notch signaling pathways in tumor development and progression. Cancer Lett (2009) 1.42

A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst Biol (2010) 1.40

Inhibition of the acetyltransferases p300 and CBP reveals a targetable function for p300 in the survival and invasion pathways of prostate cancer cell lines. Mol Cancer Ther (2011) 1.39

Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol (2010) 1.33

Revealing differences in gene network inference algorithms on the network level by ensemble methods. Bioinformatics (2010) 1.30

Subnetwork state functions define dysregulated subnetworks in cancer. J Comput Biol (2011) 1.21

Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res (2009) 1.19

Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer. PLoS Med (2010) 1.19

A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks. Genomics (2010) 1.07

OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. Nucleic Acids Res (2006) 1.06

Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Med Genomics (2011) 1.02

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics (2010) 0.98

Gene-centered regulatory networks. Brief Funct Genomics (2009) 0.98

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics (2007) 0.97

A systems biology-based classifier for hepatocellular carcinoma diagnosis. PLoS One (2011) 0.90

Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma. World J Gastroenterol (2008) 0.87

HCCNet: an integrated network database of hepatocellular carcinoma. Cell Res (2010) 0.83

Articles by these authors

Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Engl J Med (2002) 36.55

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell (2007) 17.98

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08

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

DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science (2003) 8.81

Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75

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

High-throughput genotyping by whole-genome resequencing. Genome Res (2009) 5.74

EpCAM-positive hepatocellular carcinoma cells are tumor-initiating cells with stem/progenitor cell features. Gastroenterology (2008) 5.53

A map of rice genome variation reveals the origin of cultivated rice. Nature (2012) 4.92

Analysis of Longitudinal Data with Semiparametric Estimation of Covariance Function. J Am Stat Assoc (2007) 4.68

Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population. Am J Physiol Lung Cell Mol Physiol (2002) 4.68

Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell (2011) 4.54

CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science (2006) 4.26

The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet (2011) 4.19

EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma. Cancer Res (2008) 4.17

Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87

Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet (2013) 3.83

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A (2007) 3.52

Acupuncture de qi, from qualitative history to quantitative measurement. J Altern Complement Med (2007) 3.27

Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov (2009) 3.20

Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS One (2011) 3.10

Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A (2007) 3.06

Retracted Contribution of human alpha-defensin 1, 2, and 3 to the anti-HIV-1 activity of CD8 antiviral factor. Science (2002) 2.81

PUMA regulates intestinal progenitor cell radiosensitivity and gastrointestinal syndrome. Cell Stem Cell (2008) 2.68

Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet (2011) 2.52

Exploration of gene-gene interaction effects using entropy-based methods. Eur J Hum Genet (2007) 2.42

Novel biomarkers for pre-diabetes identified by metabolomics. Mol Syst Biol (2012) 2.39

Diagnostic and prognostic implications of microRNAs in human hepatocellular carcinoma. Int J Cancer (2008) 2.35

microRNA-21 negatively regulates Cdc25A and cell cycle progression in colon cancer cells. Cancer Res (2009) 2.32

Consumption of whole grains and cereal fiber and total and cause-specific mortality: prospective analysis of 367,442 individuals. BMC Med (2015) 2.22

Influence of induced reactive oxygen species in p53-mediated cell fate decisions. Mol Cell Biol (2003) 2.16

RhoA-mediated apical actin enrichment is required for ciliogenesis and promoted by Foxj1. J Cell Sci (2007) 2.14

Salinomycin inhibits Wnt signaling and selectively induces apoptosis in chronic lymphocytic leukemia cells. Proc Natl Acad Sci U S A (2011) 2.12

In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS One (2010) 2.10

DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development (2005) 2.08

Effects and Clinical Characteristics of Intracranial Pressure Monitoring-Targeted Management for Subsets of Traumatic Brain Injury: An Observational Multicenter Study. Crit Care Med (2015) 2.06

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol (2010) 2.03

PUMA Dissociates Bax and Bcl-X(L) to induce apoptosis in colon cancer cells. J Biol Chem (2006) 2.02

Significance of serum microRNAs in pre-diabetes and newly diagnosed type 2 diabetes: a clinical study. Acta Diabetol (2010) 2.01

Following cytochrome c release, autophagy is inhibited during chemotherapy-induced apoptosis by caspase 8-mediated cleavage of Beclin 1. Cancer Res (2011) 1.99

Study of severe and rare complications of transarterial chemoembolization (TACE) for liver cancer. Eur J Radiol (2006) 1.95

Specific Btk inhibition suppresses B cell- and myeloid cell-mediated arthritis. Nat Chem Biol (2010) 1.94

A margin-negative R0 resection accomplished with minimal postoperative complications is the surgeon's contribution to long-term survival in pancreatic cancer. J Gastrointest Surg (2006) 1.89

Coupling of cell migration with neurogenesis by proneural bHLH factors. Proc Natl Acad Sci U S A (2006) 1.87

PUMA-mediated apoptosis drives chemical hepatocarcinogenesis in mice. Hepatology (2011) 1.82

Liver cancer initiation is controlled by AP-1 through SIRT6-dependent inhibition of survivin. Nat Cell Biol (2012) 1.81

A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer. Clin Cancer Res (2007) 1.77

Bispecific antibodies directed to CD4 domain 2 and HIV envelope exhibit exceptional breadth and picomolar potency against HIV-1. Proc Natl Acad Sci U S A (2013) 1.76

Molecular characterization of human immunodeficiency virus type 1 and hepatitis C virus in paid blood donors and injection drug users in china. J Virol (2004) 1.76

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res (2007) 1.76

Role of f-box factor foxj1 in differentiation of ciliated airway epithelial cells. Am J Physiol Lung Cell Mol Physiol (2003) 1.76

The nuclear function of p53 is required for PUMA-mediated apoptosis induced by DNA damage. Proc Natl Acad Sci U S A (2007) 1.73

Selection against PUMA gene expression in Myc-driven B-cell lymphomagenesis. Mol Cell Biol (2008) 1.72

En face view of atrial septal defect by two-dimensional transthoracic echocardiography: comparison to real-time three-dimensional transesophageal echocardiography. J Am Soc Echocardiogr (2010) 1.71

Notch signaling determines the M1 versus M2 polarization of macrophages in antitumor immune responses. Cancer Res (2010) 1.70

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet (2013) 1.68

Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiol (2009) 1.65

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet (2009) 1.64

Enhanced microtubule-dependent trafficking and p53 nuclear accumulation by suppression of microtubule dynamics. Proc Natl Acad Sci U S A (2002) 1.64

Adenosine 5'-tetraphosphate is a highly potent purinergic endothelium-derived vasoconstrictor. Circ Res (2008) 1.61

Differences between human plasma and serum metabolite profiles. PLoS One (2011) 1.61

A nomenclature for intestinal in vitro cultures. Am J Physiol Gastrointest Liver Physiol (2012) 1.61

Impact of thymectomy on the peripheral T cell pool in rhesus macaques before and after infection with simian immunodeficiency virus. Eur J Immunol (2005) 1.60

Methylation profile of the promoter CpG islands of 31 genes that may contribute to colorectal carcinogenesis. World J Gastroenterol (2004) 1.58

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet (2013) 1.58

Notch signaling promotes astrogliogenesis via direct CSL-mediated glial gene activation. J Neurosci Res (2002) 1.58

p53 independent induction of PUMA mediates intestinal apoptosis in response to ischaemia-reperfusion. Gut (2006) 1.56

Retroperitoneal laparoscopic anatrophic nephrolithotomy for large staghorn calculi. Int J Urol (2010) 1.53

Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J Theor Biol (2005) 1.51

SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics (2009) 1.51

Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics (2005) 1.50

HIT: linking herbal active ingredients to targets. Nucleic Acids Res (2010) 1.50

The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Commun (2013) 1.50

Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J (2004) 1.50

Characterizing breast cancer xenograft epidermal growth factor receptor expression by using near-infrared optical imaging. Acta Radiol (2009) 1.49

A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. Diabetes (2012) 1.47

Sp1 and p73 activate PUMA following serum starvation. Carcinogenesis (2008) 1.46

Downregulation of Dkk3 activates beta-catenin/TCF-4 signaling in lung cancer. Carcinogenesis (2007) 1.46

Activation of the Akt-NF-kappaB pathway by subtilase cytotoxin through the ATF6 branch of the unfolded protein response. J Immunol (2009) 1.44

Ventricular fibrillation induced by transoesophageal cardiac pacing: a new model of cardiac arrest in rats. Resuscitation (2007) 1.44

Elevation of receptor tyrosine kinase EphA2 mediates resistance to trastuzumab therapy. Cancer Res (2009) 1.44

PUMA-mediated intestinal epithelial apoptosis contributes to ulcerative colitis in humans and mice. J Clin Invest (2011) 1.43

ITFP: an integrated platform of mammalian transcription factors. Bioinformatics (2008) 1.43

Inhibition of CDK4/6 protects against radiation-induced intestinal injury in mice. J Clin Invest (2016) 1.43

Prognostic role of serum carbohydrate antigen 19-9 levels in patients with resectable hepatocellular carcinoma. Tumour Biol (2015) 1.42

Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids (2011) 1.41

Optical signature of symmetry variations and spin-valley coupling in atomically thin tungsten dichalcogenides. Sci Rep (2013) 1.41

Epinephrine, but not vasopressin, improves survival rates in an adult rabbit model of asphyxia cardiac arrest. Am J Emerg Med (2007) 1.41