Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk.

PubWeight™: 0.81‹?›

🔗 View Article (PMC 3061120)

Published in J R Soc Interface on October 13, 2010

Authors

Yan Xu1, Wen Hu, Zhiqiang Chang, Huizi Duanmu, Shanzhen Zhang, Zhenqi Li, Zihui Li, Lili Yu, Xia Li

Author Affiliations

1: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, People's Republic of China. xuyanls@yahoo.com.cn

Articles cited by this

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37

The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67

Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25

Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell (1997) 16.79

Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69

An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42

PID: the Pathway Interaction Database. Nucleic Acids Res (2008) 12.92

The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer (2004) 12.35

Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature (2008) 12.01

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74

The IntAct molecular interaction database in 2010. Nucleic Acids Res (2009) 9.85

Genes that mediate breast cancer metastasis to the brain. Nature (2009) 8.23

Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell (2008) 7.80

Computational prediction of human metabolic pathways from the complete human genome. Genome Biol (2004) 7.52

MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74

Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10

Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol (2005) 5.38

A text-mining analysis of the human phenome. Eur J Hum Genet (2006) 4.98

Combining multiple microarray studies and modeling interstudy variation. Bioinformatics (2003) 4.38

Genome-wide prediction of C. elegans genetic interactions. Science (2006) 4.15

InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15

Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99

Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia. Blood (2008) 3.89

An anti-apoptotic role for the p53 family member, p73, during developmental neuron death. Science (2000) 3.12

The involvement of IL-1 in tumorigenesis, tumor invasiveness, metastasis and tumor-host interactions. Cancer Metastasis Rev (2006) 2.74

A global pathway crosstalk network. Bioinformatics (2008) 2.27

Microarray analysis of altered sphingolipid metabolism reveals prognostic significance of sphingosine kinase 1 in breast cancer. Breast Cancer Res Treat (2007) 2.01

InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res (2003) 1.94

PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91

E2F family members are differentially regulated by reversible acetylation. J Biol Chem (2000) 1.77

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

Defective brain development in mice lacking the Hif-1alpha gene in neural cells. Mol Cell Biol (2003) 1.75

How cohesin and CTCF cooperate in regulating gene expression. Chromosome Res (2009) 1.62

Interaction of survival and death signaling in basal forebrain neurons: roles of neurotrophins and proneurotrophins. J Neurosci (2006) 1.58

RbAp48 belongs to the histone deacetylase complex that associates with the retinoblastoma protein. J Biol Chem (2000) 1.56

Brain-derived neurotrophic factor activation of TrkB induces vascular endothelial growth factor expression via hypoxia-inducible factor-1alpha in neuroblastoma cells. Cancer Res (2006) 1.53

DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res (2009) 1.41

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics (2006) 1.35

Cross-talk between the androgen receptor and the phosphatidylinositol 3-kinase/Akt pathway in prostate cancer. Curr Cancer Drug Targets (2007) 1.34

Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31

Inhibition of N-linked glycosylation disrupts receptor tyrosine kinase signaling in tumor cells. Cancer Res (2008) 1.26

Dual regulatory roles of phosphatidylinositol 3-kinase in IFN signaling. J Immunol (2008) 1.22

Crystal structure of the neurotrophin-3 and p75NTR symmetrical complex. Nature (2008) 1.18

Down-regulation of sphingosine kinase-1 by DNA damage: dependence on proteases and p53. J Biol Chem (2004) 1.15

Aryl hydrocarbon receptor inhibition downregulates the TGF-beta/Smad pathway in human glioblastoma cells. Oncogene (2009) 1.13

Histone deacetylases: focus on the nervous system. Cell Mol Life Sci (2007) 1.13

Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res (2005) 1.09

Syndecan-2 is expressed in the microvasculature of gliomas and regulates angiogenic processes in microvascular endothelial cells. J Biol Chem (2006) 1.07

Androgen receptor interacts with telomeric proteins in prostate cancer cells. J Biol Chem (2010) 0.97

Phosphoinositide 3-kinase regulates a subset of interferon-alpha-stimulated genes. Exp Cell Res (2006) 0.88

Neuroendocrine and immune mediators in prostate cancer progression. Front Biosci (1998) 0.85

IL-12 treatment of endogenously arising murine brain tumors. J Immunol (2000) 0.76

Articles by these authors

APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res (2008) 4.23

Pivotal role of dermal IL-17-producing γδ T cells in skin inflammation. Immunity (2011) 3.75

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet (2011) 3.68

A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet (2006) 3.24

China: the aging giant. J Am Geriatr Soc (2007) 2.89

Integrated circuits based on bilayer MoS₂ transistors. Nano Lett (2012) 2.63

Estimating species phylogenies using coalescence times among sequences. Syst Biol (2009) 2.42

Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol (2009) 2.14

Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics (2005) 2.01

Human immunodeficiency virus type 1 enters brain microvascular endothelia by macropinocytosis dependent on lipid rafts and the mitogen-activated protein kinase signaling pathway. J Virol (2002) 1.97

MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res (2010) 1.94

Transmission of MDR and XDR tuberculosis in Shanghai, China. PLoS One (2009) 1.93

Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque. Nat Genet (2011) 1.92

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol (2010) 1.92

Brain cannabinoid CB₂ receptors modulate cocaine's actions in mice. Nat Neurosci (2011) 1.88

Major taste loss in carnivorous mammals. Proc Natl Acad Sci U S A (2012) 1.81

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest (2013) 1.76

trans-Diaqua-bis[5-carb-oxy-4-carboxyl-ato-2-(4-pyridinio)-1H-imidazol-1-ido-κN,O]iron(II). Acta Crystallogr Sect E Struct Rep Online (2009) 1.72

Correlation of iron in the hippocampus with MMSE in patients with Alzheimer's disease. J Magn Reson Imaging (2009) 1.64

High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases. Nucleic Acids Res (2013) 1.61

The Highwire ubiquitin ligase promotes axonal degeneration by tuning levels of Nmnat protein. PLoS Biol (2012) 1.60

Integrin-mediated type II TGF-β receptor tyrosine dephosphorylation controls SMAD-dependent profibrotic signaling. J Clin Invest (2014) 1.59

MiR-27a modulates MDR1/P-glycoprotein expression by targeting HIPK2 in human ovarian cancer cells. Gynecol Oncol (2010) 1.55

Effect of transcutaneous auricular vagus nerve stimulation on impaired glucose tolerance: a pilot randomized study. BMC Complement Altern Med (2014) 1.54

Uptake, recycling, and antioxidant actions of alpha-lipoic acid in endothelial cells. Free Radic Biol Med (2002) 1.54

Allogeneic mesenchymal stem cell transplantation in severe and refractory systemic lupus erythematosus: 4 years of experience. Cell Transplant (2013) 1.53

Association between IGF2BP2 rs4402960 polymorphism and risk of type 2 diabetes mellitus: a meta-analysis. Arch Med Res (2011) 1.49

Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics (2008) 1.48

Cross-priming amplification for rapid detection of Mycobacterium tuberculosis in sputum specimens. J Clin Microbiol (2008) 1.47

A silica sol-gel design strategy for nanostructured metallic materials. Nat Mater (2012) 1.47

Cannabinoid CB1 receptor antagonist AM251 inhibits cocaine-primed relapse in rats: role of glutamate in the nucleus accumbens. J Neurosci (2006) 1.46

Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. Bioinformatics (2008) 1.46

SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res (2009) 1.45

Vascular endothelial growth factor (VEGF) +936 C/T gene polymorphisms and gastric cancer risk: a meta-analysis involving 4,138 subjects. Int J Biol Markers (2010) 1.43

Allelic variation of the Tas1r3 taste receptor gene selectively affects behavioral and neural taste responses to sweeteners in the F2 hybrids between C57BL/6ByJ and 129P3/J mice. J Neurosci (2004) 1.43

Sem1, the yeast ortholog of a human BRCA2-binding protein, is a component of the proteasome regulatory particle that enhances proteasome stability. J Cell Sci (2004) 1.42

Overexpression of EZH2 contributes to acquired cisplatin resistance in ovarian cancer cells in vitro and in vivo. Cancer Biol Ther (2010) 1.37

QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res (2011) 1.37

Galectin-3 in cardiac remodeling and heart failure. Curr Heart Fail Rep (2010) 1.37

Plasticity in eucaryotic 20S proteasome ring assembly revealed by a subunit deletion in yeast. EMBO J (2004) 1.34

Disruption of the cellulose synthase gene, AtCesA8/IRX1, enhances drought and osmotic stress tolerance in Arabidopsis. Plant J (2005) 1.34

Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. Cell Res (2010) 1.33

The CB1 receptor antagonist SR141716A selectively increases monoaminergic neurotransmission in the medial prefrontal cortex: implications for therapeutic actions. Br J Pharmacol (2003) 1.33

The relationship between body mass index and hip osteoarthritis: a systematic review and meta-analysis. Joint Bone Spine (2010) 1.33

Female oxytocin-deficient mice display enhanced anxiety-related behavior. Endocrinology (2003) 1.32

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer. J Pathol (2014) 1.31

Estimating species trees from unrooted gene trees. Syst Biol (2011) 1.31

Genomic insights into salt adaptation in a desert poplar. Nat Commun (2013) 1.30

Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochem Biophys Res Commun (2008) 1.30

Correlation of three-dimensional structures with the antibacterial activity of a group of peptides designed based on a nontoxic bacterial membrane anchor. J Biol Chem (2004) 1.30

A robust hybrid between genetic algorithm and support vector machine for extracting an optimal feature gene subset. Genomics (2005) 1.30

Heavy metal sources identification and sampling uncertainty analysis in a field-scale vegetable soil of Hangzhou, China. Environ Pollut (2008) 1.29

The Salt Overly Sensitive (SOS) pathway: established and emerging roles. Mol Plant (2013) 1.28

Allelic variation of the Tas1r3 taste receptor gene selectively affects taste responses to sweeteners: evidence from 129.B6-Tas1r3 congenic mice. Physiol Genomics (2007) 1.28

HHMD: the human histone modification database. Nucleic Acids Res (2009) 1.27

NDRG2 expression and mutation in human liver and pancreatic cancers. World J Gastroenterol (2004) 1.27

Anxiogenic effects of cocaine withdrawal in zebrafish. Physiol Behav (2007) 1.27

A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana. J Exp Bot (2010) 1.24

Isotretinoin-loaded solid lipid nanoparticles with skin targeting for topical delivery. Int J Pharm (2006) 1.24

An endoplasmic reticulum response pathway mediates programmed cell death of root tip induced by water stress in Arabidopsis. New Phytol (2010) 1.23

KLF6 induces apoptosis in prostate cancer cells through up-regulation of ATF3. J Biol Chem (2008) 1.23

Association between NSAIDs use and breast cancer risk: a systematic review and meta-analysis. Breast Cancer Res Treat (2008) 1.22

N-Myc downstream-regulated gene 2 is involved in p53-mediated apoptosis. Nucleic Acids Res (2008) 1.22

Umbilical cord mesenchymal stem cell transplantation in active and refractory systemic lupus erythematosus: a multicenter clinical study. Arthritis Res Ther (2014) 1.22

Cannabinoid CB1 receptor antagonists attenuate cocaine's rewarding effects: experiments with self-administration and brain-stimulation reward in rats. Neuropsychopharmacology (2007) 1.21

Maximum tree: a consistent estimator of the species tree. J Math Biol (2009) 1.20

Down-regulation of TIPE2 mRNA expression in peripheral blood mononuclear cells from patients with systemic lupus erythematosus. Clin Immunol (2009) 1.20

The analysis of the drug-targets based on the topological properties in the human protein-protein interaction network. J Drug Target (2009) 1.20

Salt modulates gravity signaling pathway to regulate growth direction of primary roots in Arabidopsis. Plant Physiol (2007) 1.17

Development and evaluation of silk fibroin-based nerve grafts used for peripheral nerve regeneration. Biomaterials (2007) 1.17

Association between embB codon 306 mutations and drug resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother (2007) 1.17

A regulatory effect of IL-21 on T follicular helper-like cell and B cell in rheumatoid arthritis. Arthritis Res Ther (2012) 1.17

YQA14: a novel dopamine D3 receptor antagonist that inhibits cocaine self-administration in rats and mice, but not in D3 receptor-knockout mice. Addict Biol (2011) 1.16

Gene therapy following subretinal AAV5 vector delivery is not affected by a previous intravitreal AAV5 vector administration in the partner eye. Mol Vis (2009) 1.16

Overexpression of SOS (Salt Overly Sensitive) genes increases salt tolerance in transgenic Arabidopsis. Mol Plant (2008) 1.16

Synthesis and transfer of single-layer transition metal disulfides on diverse surfaces. Nano Lett (2013) 1.16

Screening of oleaginous yeast strains tolerant to lignocellulose degradation compounds. Appl Biochem Biotechnol (2009) 1.15

Is K-ras gene mutation a prognostic factor for colorectal cancer: a systematic review and meta-analysis. Dis Colon Rectum (2012) 1.15

IDH1/2 mutations target a key hallmark of cancer by deregulating cellular metabolism in glioma. Neuro Oncol (2013) 1.15

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering. BMC Genomics (2007) 1.15

H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev (2013) 1.14

Science and Government. Reforming China's S&T system. Science (2013) 1.14

Arabidopsis EIN2 modulates stress response through abscisic acid response pathway. Plant Mol Biol (2007) 1.14

Accuracy of image registration between MRI and light microscopy in the ex vivo brain. Magn Reson Imaging (2011) 1.14

Prioritizing candidate disease miRNAs by topological features in the miRNA target-dysregulated network: case study of prostate cancer. Mol Cancer Ther (2011) 1.14

Inhibition of aberrant circulating Tfh cell proportions by corticosteroids in patients with systemic lupus erythematosus. PLoS One (2012) 1.13

Dog sciatic nerve regeneration across a 30-mm defect bridged by a chitosan/PGA artificial nerve graft. Brain (2005) 1.12

Quantitative effects of common genetic variations in the 3'UTR of the human LDL-receptor gene and their associations with plasma lipid levels in the Atherosclerosis Risk in Communities study. Hum Genet (2007) 1.12

Inhibition of NAALADase by 2-PMPA attenuates cocaine-induced relapse in rats: a NAAG-mGluR2/3-mediated mechanism. J Neurochem (2009) 1.11

Loci on chromosomes 2, 4, 9, and 16 for body weight, body length, and adiposity identified in a genome scan of an F2 intercross between the 129P3/J and C57BL/6ByJ mouse strains. Mamm Genome (2003) 1.11

Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. Nucleic Acids Res (2013) 1.11

Expression profiling of murine acute promyelocytic leukemia cells reveals multiple model-dependent progression signatures. Mol Cell Biol (2004) 1.10

A Wnt-Frz/Ror-Dsh pathway regulates neurite outgrowth in Caenorhabditis elegans. PLoS Genet (2010) 1.09

Combined deficiency of vitamins E and C causes paralysis and death in guinea pigs. Am J Clin Nutr (2003) 1.09

Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett (2008) 1.09

Prevalence of fluoroquinolone resistance among tuberculosis patients in Shanghai, China. Antimicrob Agents Chemother (2009) 1.09

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression. Bioinformatics (2012) 1.08

Selection of mutations to detect multidrug-resistant Mycobacterium tuberculosis strains in Shanghai, China. Antimicrob Agents Chemother (2009) 1.08

Clinical manifestations of dermatomyositis and clinically amyopathic dermatomyositis patients with positive expression of anti-melanoma differentiation-associated gene 5 antibody. Arthritis Care Res (Hoboken) (2012) 1.08