Published in Plant Cell Physiol on December 10, 2013
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic Acids Res (2014) 1.14
ABCG transporters are required for suberin and pollen wall extracellular barriers in Arabidopsis. Plant Cell (2014) 1.06
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. Plant Cell Physiol (2015) 1.00
MOROKOSHI: transcriptome database in Sorghum bicolor. Plant Cell Physiol (2014) 0.96
MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage. Plant Physiol (2015) 0.94
Triticeae resources in Ensembl Plants. Plant Cell Physiol (2014) 0.92
Glycosylinositol phosphorylceramides from Rosa cell cultures are boron-bridged in the plasma membrane and form complexes with rhamnogalacturonan II. Plant J (2014) 0.92
The Biosynthetic Pathway of Indole-3-Carbaldehyde and Indole-3-Carboxylic Acid Derivatives in Arabidopsis. Plant Physiol (2014) 0.91
Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Front Plant Sci (2014) 0.91
Systems biology in the context of big data and networks. Biomed Res Int (2014) 0.90
A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. DNA Res (2016) 0.87
Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. Plant Cell Physiol (2014) 0.86
Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners. Plant Physiol (2014) 0.85
ImmuCo: a database of gene co-expression in immune cells. Nucleic Acids Res (2014) 0.84
Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana. J Exp Bot (2016) 0.82
Learning from Co-expression Networks: Possibilities and Challenges. Front Plant Sci (2016) 0.81
The conserved transcription factors, MYB115 and MYB118, control expression of the newly evolved benzoyloxy glucosinolate pathway in Arabidopsis thaliana. Front Plant Sci (2015) 0.81
Crop improvement using life cycle datasets acquired under field conditions. Front Plant Sci (2015) 0.78
ALA10, a Phospholipid Flippase, Controls FAD2/FAD3 Desaturation of Phosphatidylcholine in the ER and Affects Chloroplast Lipid Composition in Arabidopsis thaliana. Plant Physiol (2015) 0.78
New insights into the evolutionary history of plant sorbitol dehydrogenase. BMC Plant Biol (2015) 0.77
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system. Proc Natl Acad Sci U S A (2016) 0.77
Bioinformatic landscapes for plant transcription factor system research. Planta (2015) 0.77
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. Plant Cell Physiol (2014) 0.77
Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. PLoS Genet (2016) 0.77
Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. Front Plant Sci (2015) 0.76
Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance. BMC Plant Biol (2016) 0.76
Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Plant Signal Behav (2014) 0.76
"PP2C7s", Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases. PLoS One (2015) 0.75
ALCOdb: Gene Coexpression Database for Microalgae. Plant Cell Physiol (2015) 0.75
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. BMC Plant Biol (2017) 0.75
Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1. Plant Physiol (2017) 0.75
Small One-Helix Proteins Are Essential for Photosynthesis in Arabidopsis. Front Plant Sci (2017) 0.75
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. Plant Cell Physiol (2015) 0.75
DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One (2017) 0.75
A Proteomic View on the Role of Legume Symbiotic Interactions. Front Plant Sci (2017) 0.75
RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes. Evol Bioinform Online (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Food security: the challenge of feeding 9 billion people. Science (2010) 22.51
A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol (2010) 22.10
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32
GenBank. Nucleic Acids Res (2012) 10.89
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res (2011) 7.93
The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J (2005) 6.07
Synteny and collinearity in plant genomes. Science (2008) 5.26
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
Analyzing a portion of the ROC curve. Med Decis Making (1989) 3.87
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res (2008) 3.70
Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol (2007) 3.13
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ (2009) 2.76
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol (2013) 2.28
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell (2011) 2.13
Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res (2009) 2.11
Tissue-specific codon usage and the expression of human genes. Proc Natl Acad Sci U S A (2004) 1.91
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res (2010) 1.82
GeneCAT--novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res (2008) 1.70
ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol (2011) 1.67
COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res (2010) 1.50
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. Nucleic Acids Res (2012) 1.46
CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics (2010) 1.32
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol (2010) 1.30
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics (2009) 1.28
Similarities of ordered gene lists. J Bioinform Comput Biol (2006) 1.26
Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol (2011) 1.21
BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J (2012) 1.20
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics (2009) 1.17
Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics (2008) 1.15
Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol (2008) 1.08
Universal function-specificity of codon usage. Nucleic Acids Res (2009) 1.02
The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana. Genetics (2012) 0.90
PLANEX: the plant co-expression database. BMC Plant Biol (2013) 0.89
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res (2008) 3.70
COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res (2007) 2.86
PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res (2007) 2.59
Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res (2009) 2.11
Prediction of disordered regions in proteins based on the meta approach. Bioinformatics (2008) 2.09
Diagnosis and management of insulinoma. World J Gastroenterol (2013) 1.82
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res (2010) 1.82
ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol (2011) 1.67
Synthetic double-stranded RNA poly(I:C) combined with mucosal vaccine protects against influenza virus infection. J Virol (2005) 1.67
Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins (2004) 1.57
Two cases of systemic lupus erythematosus complicated with colonic ulcers. Intern Med (2005) 1.56
Renal outcome and predictors of clinical renal involvement in patients with silent lupus nephritis. Nephron Clin Pract (2004) 1.52
Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol (2003) 1.52
COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res (2010) 1.50
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. Nucleic Acids Res (2012) 1.46
Crucial role of the interleukin-6/interleukin-17 cytokine axis in the induction of arthritis by glucose-6-phosphate isomerase. Arthritis Rheum (2008) 1.43
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics (2004) 1.36
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res (2004) 1.25
Hub promiscuity in protein-protein interaction networks. Int J Mol Sci (2010) 1.22
Thrombosis in inferior vena cava (IVC) due to intra-cystic hemorrhage into a hepatic local cyst with autosomal dominant polycystic kidney disease (ADPKD). Intern Med (2004) 1.22
PiSite: a database of protein interaction sites using multiple binding states in the PDB. Nucleic Acids Res (2008) 1.21
Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform (2008) 1.19
A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese. PLoS Genet (2012) 1.17
Association of TNFAIP3 interacting protein 1, TNIP1 with systemic lupus erythematosus in a Japanese population: a case-control association study. Arthritis Res Ther (2010) 1.17
Role of STAT4 polymorphisms in systemic lupus erythematosus in a Japanese population: a case-control association study of the STAT1-STAT4 region. Arthritis Res Ther (2008) 1.16
Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci (2008) 1.14
Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci (2004) 1.13
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
Glucagon-like peptide-1 inhibits LPS-induced IL-1beta production in cultured rat astrocytes. Neurosci Res (2006) 1.12
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Protein Sci (2003) 1.09
Handling technology of Mega-Watt millimeter-waves for optimized heating of fusion plasmas. J Microw Power Electromagn Energy (2009) 1.09
A case of renal cell carcinoma found after skin metastasis. Hinyokika Kiyo (2004) 1.08
Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels. Circ Res (2002) 1.08
The Tohoku Medical Megabank Project: Design and Mission. J Epidemiol (2016) 1.08
Replication of the association between the C8orf13-BLK region and systemic lupus erythematosus in a Japanese population. Arthritis Rheum (2009) 1.07
Anti-interleukin-6 receptor antibody (tocilizumab) treatment of multicentric Castleman's disease. Intern Med (2007) 1.05
Therapeutic effects of antibodies to tumor necrosis factor-alpha, interleukin-6 and cytotoxic T-lymphocyte antigen 4 immunoglobulin in mice with glucose-6-phosphate isomerase induced arthritis. Arthritis Res Ther (2008) 1.04
Protection against influenza virus infection by intranasal administration of C3d-fused hemagglutinin. Vaccine (2003) 1.03
TLR7 single-nucleotide polymorphisms in the 3' untranslated region and intron 2 independently contribute to systemic lupus erythematosus in Japanese women: a case-control association study. Arthritis Res Ther (2011) 1.02
Interleukin-6 gene promoter methylation in rheumatoid arthritis and chronic periodontitis. J Periodontol (2011) 1.01
Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng Des Sel (2006) 1.00
Time-dependent increased risk for serious infection from continuous use of tumor necrosis factor antagonists over three years in patients with rheumatoid arthritis. Arthritis Care Res (Hoboken) (2012) 1.00
Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network. Protein Sci (2010) 0.99
Classification and characteristics of Japanese patients with antineutrophil cytoplasmic antibody-associated vasculitis in a nationwide, prospective, inception cohort study. Arthritis Res Ther (2014) 0.98
Use of laser microdissection in the analysis of renal-infiltrating T cells in MRL/lpr mice. Mod Rheumatol (2008) 0.97
Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol (2004) 0.97
Regulatory polymorphisms in EGR2 are associated with susceptibility to systemic lupus erythematosus. Hum Mol Genet (2010) 0.97
Nuclear localization of beta-catenin involved in precancerous change in oral leukoplakia. Mol Cancer (2007) 0.96
Arthritogenic T cell epitope in glucose-6-phosphate isomerase-induced arthritis. Arthritis Res Ther (2008) 0.96
Interleukin-17 gene expression in patients with rheumatoid arthritis. Mod Rheumatol (2007) 0.94
Antibody responses to periodontopathic bacteria in relation to rheumatoid arthritis in Japanese adults. J Periodontol (2011) 0.94
Pathogenic role of immune response to M3 muscarinic acetylcholine receptor in Sjögren's syndrome-like sialoadenitis. J Autoimmun (2010) 0.94
DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res (2006) 0.93
Association of a functional polymorphism in the 3'-untranslated region of SPI1 with systemic lupus erythematosus. Arthritis Rheum (2011) 0.93
Overexpression of phosphorylated STAT-1alpha in the labial salivary glands of patients with Sjögren's syndrome. Arthritis Rheum (2006) 0.93
Periodontal treatment decreases levels of antibodies to Porphyromonas gingivalis and citrulline in patients with rheumatoid arthritis and periodontitis. J Periodontol (2013) 0.93
Drug retention rates and relevant risk factors for drug discontinuation due to adverse events in rheumatoid arthritis patients receiving anticytokine therapy with different target molecules. Ann Rheum Dis (2012) 0.92
Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics (2010) 0.91
Mizoribine therapy for patients with lupus nephritis: the association between peak mizoribine concentration and clinical efficacy. Mod Rheumatol (2007) 0.91
Cartilage repair in transplanted scaffold-free chondrocyte sheets using a minipig model. Biomaterials (2012) 0.91
Comparative suppressive effects of tyrosine kinase inhibitors imatinib and nilotinib in models of autoimmune arthritis. Mod Rheumatol (2010) 0.90
Blind prediction of interfacial water positions in CAPRI. Proteins (2013) 0.90
DNA microarray analysis of labial salivary glands of patients with Sjogren's syndrome. Ann Rheum Dis (2007) 0.90
p16 promoter methylation in the serum as a basis for the molecular diagnosis of gliomas. Neurosurgery (2009) 0.90
Pulmonary diffusion capacity in patients with systemic lupus erythematosus. Respirology (2002) 0.90
Seasonal changes in canopy photosynthesis and respiration, and partitioning of photosynthate, in rice (Oryza sativa L.) grown under free-air CO2 enrichment. Plant Cell Physiol (2005) 0.90
A cavity with an appropriate size is the basis of the PPIase activity. Protein Eng Des Sel (2008) 0.89
Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase. Plant J (2002) 0.89
Cytokine gene polymorphisms associated with rheumatoid arthritis and periodontitis in Japanese adults. J Periodontol (2009) 0.89
The interleukin-1 and Fcgamma receptor gene polymorphisms in Japanese patients with rheumatoid arthritis and periodontitis. J Periodontol (2007) 0.89
Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel. PLoS One (2013) 0.89
Docking of protein molecular surfaces with evolutionary trace analysis. Proteins (2007) 0.89
Replication of association between FAM167A(C8orf13)-BLK region and rheumatoid arthritis in a Japanese population. Ann Rheum Dis (2009) 0.89
Perfusion through the dorsalis pedis artery for acute limb ischemia secondary to an occlusive arterial cannula during percutaneous cardiopulmonary support. J Artif Organs (2005) 0.89
Association of TNFAIP3 polymorphism with susceptibility to systemic lupus erythematosus in a Japanese population. J Biomed Biotechnol (2010) 0.88
Sarcoid myositis with muscle weakness as a presenting symptom. Mod Rheumatol (2007) 0.88
Development of virtual reality exercise of hand motion assist robot for rehabilitation therapy by patient self-motion control. Conf Proc IEEE Eng Med Biol Soc (2008) 0.88
Spontaneously ruptured craniopharyngioma cyst without meningitic symptoms --two case reports. Neurol Med Chir (Tokyo) (2003) 0.88
In vivo detection of amyloid plaques in the mouse brain using the near-infrared fluorescence probe THK-265. J Alzheimers Dis (2011) 0.87
A case of pneumatosis cystoides intestinalis in a patient with polymyositis and interstitial pneumonia. Mod Rheumatol (2004) 0.87
Decreased 18F-FDG uptake 1 day after initiation of chemotherapy for malignant lymphomas. J Nucl Med (2004) 0.86
The combined genotypes of stimulatory and inhibitory Fc gamma receptors associated with systemic lupus erythematosus and periodontitis in Japanese adults. J Periodontol (2007) 0.86
Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks. BMC Genomics (2011) 0.85
Use of telemedicine in periodic screening of diabetic retinopathy. Telemed J E Health (2003) 0.85
Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions. J Chem Inf Model (2012) 0.85
Assessment of interleukin-6 receptor inhibition therapy on periodontal condition in patients with rheumatoid arthritis and chronic periodontitis. J Periodontol (2013) 0.85
A functional variant of Fcgamma receptor IIIA is associated with rheumatoid arthritis in individuals who are positive for anti-glucose-6-phosphate isomerase antibodies. Arthritis Res Ther (2005) 0.85
Risk of periodontitis in systemic lupus erythematosus is associated with Fcgamma receptor polymorphisms. J Periodontol (2003) 0.85
Protection against influenza virus infection by intranasal vaccine with surf clam microparticles (SMP) as an adjuvant. J Med Virol (2006) 0.85
The role of bone marrow-derived cells during the bone healing process in the GFP mouse bone marrow transplantation model. Calcif Tissue Int (2012) 0.84