ConsensusPathDB--a database for integrating human functional interaction networks.
paper
Cited
Public
- Authors
- Kamburov, Atanas; Wierling, Christoph; Lehrach, Hans; Herwig, Ralf
- Year
- 2009
- Journal
- Nucleic acids research
- PMID
- 18940869
- DOI
- 10.1093/nar/gkn698
- PMCID
- PMC2686562
ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26,133 distinct physical entities and 74,289 distinct functional interactions (protein-protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de.
Graphical summary of the main functions of the ConsensusPathDB web interface. The search for interactions of specific entities or pathways, search for interaction paths, overrepresentation analysis and model upload induce specific interaction subnetworks that can be visualized in the dynamic visualization environment and exported in BioPAX format for further computational analysis, or as images. Different colors of nodes and edges refer to different types of interactions or entities and different source databases, respectively. The background image shows a screenshot of the ConsensusPathDB start page.
Illustration of the mapping procedure. Two biochemical reactions that are identical according to their primary participants and the user-specified mapping criteria are mapped. The reaction A + B -> C + D, catalyzed by enzyme E1, originates from database X. A similar reaction, catalyzed by enzymes E1 and E2, originates from database Y. Since both reactions are identical according to the user-specified rules, the interactions are merged and visualized reflecting the source annotations.
| # | Section | Preview |
|---|---|---|
| 20 | SUPPLEMENTARY DATA | Supplementary Data are available at NAR Online. |
| 21 | FUNDING | This work was supported by the EMBRACE and CARCINOGENOMICS projects that are funded by the European⦠|
| 22 | FUNDING | Conflict of interest statement. None declared. |
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| Toxicity and Metabolomic Impact of Cobalt, Chromium, and Nickel Exposure on HepaRG Hepatocytes. | Bellouard M et al. | β | 2022 | β |
| 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer. | Peck B et al. | β | 2021 | β |
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| Age-Related Neurometabolomic Signature of Mouse Brain. | Chen S et al. | β | 2021 | β |
| A metabolome atlas of the aging mouse brain. | Ding J et al. | β | 2021 | β |
| An integrated approach to identify environmental modulators of genetic risk factors for complex traits. | Balliu B et al. | β | 2021 | β |
| An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case. | Oommen AM et al. | β | 2021 | β |
| Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. | Ma F et al. | β | 2021 | β |
| Applying Proteomics and Integrative "Omics" Strategies to Decipher the Chronic Kidney Disease-Related Atherosclerosis. | Tracz J et al. | β | 2021 | β |
| A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. | Bow A | β | 2021 | β |
| Classification of bladder cancer cell lines according to regulon activity. | Eray A et al. | β | 2021 | β |
| Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. | Han J et al. | β | 2021 | β |
| Conserved DNA sequence features underlie pervasive RNA polymerase pausing. | Gajos M et al. | β | 2021 | β |
| Decoding disease: from genomes to networks to phenotypes. | Wong AK et al. | β | 2021 | β |
| Differential reprogramming of breast cancer subtypes in 3D cultures and implications for sensitivity to targeted therapy. | Koedoot E et al. | β | 2021 | β |
| Efficient antisense inhibition reveals microRNA-155 to restrain a late-myeloid inflammatory programme in primary human phagocytes. | Linden G et al. | β | 2021 | β |
| Epigenomic mediation after adverse childhood experiences: a systematic review and meta-analysis. | Neves I et al. | β | 2021 | β |
| Familiarity Breeds Strategy: In Silico Untangling of the Molecular Complexity on Course of Autoimmune Liver Disease-to-Hepatocellular Carcinoma Transition Predicts Novel Transcriptional Signatures. | Mukherjee S et al. | β | 2021 | β |
| Functional Prediction of Long Noncoding RNAs in Cutaneous Melanoma Using a Systems Biology Approach. | Shahmoradi M et al. | β | 2021 | β |
| Genome-wide identification of microRNA targets reveals positive regulation of the Hippo pathway by miR-122 during liver development. | Zhang Y et al. | β | 2021 | β |
| Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete <i>Chaetomium thermophilum</i>. | Singh A et al. | β | 2021 | β |
| Highly deregulated lncRNA LOC is associated with overall worse prognosis in Hepatocellular Carcinoma patients. | Lim LJ et al. | β | 2021 | β |
| Interferon-Ξ»3 Exacerbates the Inflammatory Response to Microbial Ligands: Implications for SARS-CoV-2 Pathogenesis. | Read SA et al. | β | 2021 | β |
| Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction. | Alhassen S et al. | β | 2021 | β |
| Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. | Mayneris-Perxachs J et al. | β | 2021 | β |
| Learning epistatic gene interactions from perturbation screens. | Elmes K et al. | β | 2021 | β |
| Multi-Omics Approaches to Define Calcific Aortic Valve Disease Pathogenesis. | Blaser MC et al. | β | 2021 | β |
| Multi-omics integration in biomedical research - A metabolomics-centric review. | WΓΆrheide MA et al. | β | 2021 | β |
| Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. | Wieder C et al. | β | 2021 | β |
| Proteomic blood profiling in mild, severe and critical COVID-19 patients. | Patel H et al. | β | 2021 | β |
| Proteomic signature of the Dravet syndrome in the genetic Scn1a-A1783V mouse model. | Miljanovic N et al. | β | 2021 | β |
| RAS mutations drive proliferative chronic myelomonocytic leukemia via a KMT2A-PLK1 axis. | Carr RM et al. | β | 2021 | β |
| Reprogramming of m<sup>6</sup>A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia. | Wang YJ et al. | β | 2021 | β |
| Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. | Cole JJ et al. | β | 2021 | β |
| Secretory Mucin 5AC Promotes Neoplastic Progression by Augmenting KLF4-Mediated Pancreatic Cancer Cell Stemness. | Ganguly K et al. | β | 2021 | β |
| Statins Enhance the Molecular Response in Chronic Myeloid Leukemia when Combined with Tyrosine Kinase Inhibitors. | Jang HJ et al. | β | 2021 | β |
| Statistical and bioinformatic analysis of hemimethylation patterns in non-small cell lung cancer. | Sun S et al. | β | 2021 | β |
| The 2021 update of the EPA's adverse outcome pathway database. | Mortensen HM et al. | β | 2021 | β |
| Transcriptome Analysis Identifies GATA3-AS1 as a Long Noncoding RNA Associated with Resistance to Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer Patients. | Contreras-Espinosa L et al. | β | 2021 | β |
| Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection. | Oommen A et al. | β | 2021 | β |
| Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. | Kumar A et al. | β | 2021 | β |
| Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. | Lucas-SΓ‘nchez M et al. | β | 2021 | β |
| Active constituents and mechanisms of Respiratory Detox Shot, a traditional Chinese medicine prescription, for COVID-19 control and prevention: Network-molecular docking-LC-MS<sup>E</sup> analysis. | Zhang ZJ et al. | β | 2020 | β |
| Alteration of Proteotranscriptomic Landscape Reveals the Transcriptional Regulatory Circuits Controlling Key-Signaling Pathways and Metabolic Reprogramming During Tumor Evolution. | Andrieux G et al. | β | 2020 | β |
| An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during <i>Salmonella</i> Infection. | Schulte LN et al. | β | 2020 | β |
| A Prognostic Gene-Expression Signature and Risk Score for Meningioma Recurrence After Resection. | Chen WC et al. | β | 2020 | β |
| Brief Report: A Gene Enrichment Approach Applied to Sleep and Autism. | Abel EA et al. | β | 2020 | β |
| Co-culture with mouse embryonic fibroblasts improves maintenance of metabolic function of human small hepatocyte progenitor cells. | Sengupta S et al. | β | 2020 | β |
| Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus. | Henke C et al. | β | 2020 | β |
| DNA-methylated gene markers for colorectal cancer in TCGA database. | Zhang H et al. | β | 2020 | β |
| DRUGPATH: The Drug Gene Pathway Meta-Database. | Jaundoo R et al. | β | 2020 | β |
| Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. | Shi YQ et al. | β | 2020 | β |
| Effects of Sphingosine-1-Phosphate on Cell Viability, Differentiation, and Gene Expression of Adipocytes. | Wu X et al. | β | 2020 | β |
| Engineered niches support the development of human dendritic cells in humanized mice. | Anselmi G et al. | β | 2020 | β |
| Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. | Merid SK et al. | β | 2020 | β |
| Genome-wide transcriptome profiling of ex-vivo precision-cut slices from human pancreatic ductal adenocarcinoma. | Ghaderi M et al. | β | 2020 | β |
| Identification of <i>TP53</i> mutation associated-immunotype and prediction of survival in patients with hepatocellular carcinoma. | Shi M et al. | β | 2020 | β |
| Identification of novel prognostic alternative splicing signature in papillary renal cell carcinoma. | Duan Y et al. | β | 2020 | β |
| Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. | Erzurumluoglu AM et al. | β | 2020 | β |
| Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis. | Chen S et al. | β | 2020 | β |
| Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples. | Aberg KA et al. | β | 2020 | β |
| NetCore: a network propagation approach using node coreness. | Barel G et al. | β | 2020 | β |
| Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. | Lim LJ et al. | β | 2020 | β |
| Noncoding RNA <i>MaIL1</i> is an integral component of the TLR4-TRIF pathway. | Aznaourova M et al. | β | 2020 | β |
| Predicting new drug indications for prostate cancer: The integration of an in silico proteochemometric network pharmacology platform with patient-derived primary prostate cells. | Naeem A et al. | β | 2020 | β |
| The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. | Cui J et al. | β | 2020 | β |
| The landscape of alternative splicing in HIV-1 infected CD4 T-cells. | Byun S et al. | β | 2020 | β |
| The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. | Odia T et al. | β | 2020 | β |
| The transcriptional repressor BCL11A promotes breast cancer metastasis. | Seachrist DD et al. | β | 2020 | β |
| Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. | Bruno M et al. | β | 2020 | β |
| Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease. | Patel H et al. | β | 2020 | β |
| A Meta-Analysis of Alzheimer's Disease Brain Transcriptomic Data. | Patel H et al. | β | 2019 | β |
| Antenatal Glucocorticoid Exposure Results in Sex-Specific and Transgenerational Changes in Prefrontal Cortex Gene Transcription that Relate to Behavioural Outcomes. | Constantinof A et al. | β | 2019 | β |
| A Systematic Review of MicroRNA Expression as Biomarker of Late-Onset Alzheimer's Disease. | Herrera-Espejo S et al. | β | 2019 | β |
| Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation. | Arora R et al. | β | 2019 | β |
| Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation. | Diesch J et al. | β | 2019 | β |
| Combined Analysis of the Aberrant Epigenetic Alteration of Pancreatic Ductal Adenocarcinoma. | Xu R et al. | β | 2019 | β |
| Data-Driven Materials Science: Status, Challenges, and Perspectives. | Himanen L et al. | β | 2019 | β |
| Effects of culture condition on epigenomic profiles of brain tumor cells. | Cox MC et al. | β | 2019 | β |
| Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants. | Everson TM et al. | β | 2019 | β |
| Exposure to Dimethyl Selenide (DMSe)-Derived Secondary Organic Aerosol Alters Transcriptomic Profiles in Human Airway Epithelial Cells. | Ahmed CMS et al. | β | 2019 | β |
| Fluorescent Light Incites a Conserved Immune and Inflammatory Genetic Response within Vertebrate Organs (<i>Danio Rerio</i>, <i>Oryzias Latipes</i> and <i>Mus Musculus</i>). | Boswell M et al. | β | 2019 | β |
| Genetic Predisposition for Immune System, Hormone, and Metabolic Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Pilot Study. | Perez M et al. | β | 2019 | β |
| Genome-wide meta-analysis identifies novel gender specific loci associated with thyroid antibodies level in Croatians. | Matana A et al. | β | 2019 | β |
| Genomic knockout of alms1 in zebrafish recapitulates AlstrΓΆm syndrome and provides insight into metabolic phenotypes. | Nesmith JE et al. | β | 2019 | β |
| GWAS and systems biology analysis of depressive symptoms among smokers from the COPDGene cohort. | Heinzman JT et al. | β | 2019 | β |
| HDAC5 catalytic activity suppresses cardiomyocyte oxidative stress and NRF2 target gene expression. | Hu T et al. | β | 2019 | β |
| Hemimethylation Patterns in Breast Cancer Cell Lines. | Sun S et al. | β | 2019 | β |
| Histone deacetylase inhibitor targets CD123/CD47-positive cells and reverse chemoresistance phenotype in acute myeloid leukemia. | Yan B et al. | β | 2019 | β |
| Hyperactivity of the transcription factor Nrf2 causes metabolic reprogramming in mouse esophagus. | Fu J et al. | β | 2019 | β |
| Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data. | Xu N et al. | β | 2019 | β |
| Identifying Crohn's disease signal from variome analysis. | Wang Y et al. | β | 2019 | β |
| Impact of chronically alternating light-dark cycles on circadian clock mediated expression of cancer (glioma)-related genes in the brain. | Khan S et al. | β | 2019 | β |
| Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics. | Ong JWJ et al. | β | 2019 | β |
| In Silico Target Prediction for Small Molecules. | Byrne R et al. | β | 2019 | β |
| Integrated Analysis of Oncogenic Networks in Colorectal Cancer Identifies GUCA2A as a Molecular Marker. | Zhang H et al. | β | 2019 | β |
| Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of complex traits and disease. | Hatcher C et al. | β | 2019 | β |
| Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. | Gutierrez-Arcelus M et al. | β | 2019 | β |
| Network Medicine in the Age of Biomedical Big Data. | Sonawane AR et al. | β | 2019 | β |
| PathMe: merging and exploring mechanistic pathway knowledge. | Domingo-FernΓ‘ndez D et al. | β | 2019 | β |
| Plasma Protein and MicroRNA Biomarkers of Insulin Resistance: A Network-Based Integrative -Omics Analysis. | Choi H et al. | β | 2019 | β |
| Predicting instances of pathway ontology classes for pathway integration. | Wang LL et al. | β | 2019 | β |
| Predictive modelling using pathway scores: robustness and significance of pathway collections. | Segura-Lepe MP et al. | β | 2019 | β |
| Preeclampsia is Associated with Sex-Specific Transcriptional and Proteomic Changes in Fetal Erythroid Cells. | Masoumi Z et al. | β | 2019 | β |
| Proteogenomic Characterization of Human Early-Onset Gastric Cancer. | Mun DG et al. | β | 2019 | β |
| The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. | Mubeen S et al. | β | 2019 | β |
| Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India. | Arora R et al. | β | 2019 | β |
| Transcriptomic analysis of probable asymptomatic and symptomatic alzheimer brains. | Patel H et al. | β | 2019 | β |
| Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes. | Koedoot E et al. | β | 2019 | β |
| Understanding the Early Biological Effects of Isoprene-Derived Particulate Matter Enhanced by Anthropogenic Pollutants. | Surratt JD et al. | β | 2019 | β |
| Unique molecular signature in mucolipidosis type IV microglia. | Cougnoux A et al. | β | 2019 | β |
| Using the Pleiotropic Characteristics of Curcumin to Validate the Potential Application of a Novel Gene Expression Screening Platform. | Liao SC et al. | β | 2019 | β |
| Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy. | Nutile T et al. | β | 2019 | β |
| Why do so many genetic insults lead to Purkinje Cell degeneration and spinocerebellar ataxia? | Huang M et al. | β | 2019 | β |
| Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools. | Felgueiras J et al. | β | 2018 | β |
| A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients. | Li Yim AYF et al. | β | 2018 | β |
| AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. | Pittman ME et al. | β | 2018 | β |
| A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone. | Wang L et al. | β | 2018 | β |
| Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers robust silencing of microRNA and long non-coding RNA genes. | Janga H et al. | β | 2018 | β |
| Comparative Transcriptomic and Metagenomic Analyses of Influenza Virus-Infected Nasal Epithelial Cells From Multiple Individuals Reveal Specific Nasal-Initiated Signatures. | Tan KS et al. | β | 2018 | β |
| Differential gene expression induced by anti-cancer agent plumbagin is mediated by androgen receptor in prostate cancer cells. | Rondeau G et al. | β | 2018 | β |
| Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. | Marco-Ramell A et al. | β | 2018 | β |
| GRHL2 Is Required for Collecting Duct Epithelial Barrier Function and Renal Osmoregulation. | Hinze C et al. | β | 2018 | β |
| Identification and Validation of a Diagnostic and Prognostic Multi-Gene Biomarker Panel for Pancreatic Ductal Adenocarcinoma. | Klett H et al. | β | 2018 | β |
| Identification of early biological changes in palmitate-treated isolated human islets. | Sargsyan E et al. | β | 2018 | β |
| In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of <i>Leishmania</i>-Infected Macrophages. | Veras PST et al. | β | 2018 | β |
| Integrative analysis of gene expression and methylation data for breast cancer cell lines. | Li C et al. | β | 2018 | β |
| Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma. | Sanford T et al. | β | 2018 | β |
| Lineage dynamics of murine pancreatic development at single-cell resolution. | Byrnes LE et al. | β | 2018 | β |
| Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells. | Kundu S et al. | β | 2018 | β |
| Mapping biological process relationships and disease perturbations within a pathway network. | Stoney R et al. | β | 2018 | β |
| Mechanisms of cortisol - Substance use development associations: Hypothesis generation through gene enrichment analysis. | Marceau K et al. | β | 2018 | β |
| Nerve Injury-Induced Chronic Pain Is Associated with Persistent DNA Methylation Reprogramming in Dorsal Root Ganglion. | Garriga J et al. | β | 2018 | β |
| Network and Pathway Analysis of Toxicogenomics Data. | Barel G et al. | β | 2018 | β |
| Network spectra for drug-target identification in complex diseases: new guns against old foes. | Rai A et al. | β | 2018 | β |
| Patterns of shared signatures of recent positive selection across human populations. | Johnson KE et al. | β | 2018 | β |
| PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments. | Teo G et al. | β | 2018 | β |
| Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology. | Seyerle AA et al. | β | 2018 | β |
| Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance. | Ye Z et al. | β | 2018 | β |
| Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression. | Tareen SHK et al. | β | 2018 | β |
| Proteomic profiling of epileptogenesis in a rat model: Focus on cell stress, extracellular matrix and angiogenesis. | Keck M et al. | β | 2018 | β |
| PTEN deficiency promotes pathological vascular remodeling of human coronary arteries. | Moulton KS et al. | β | 2018 | β |
| Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. | Ε alovskΓ‘ B et al. | β | 2018 | β |
| Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles. | Klett H et al. | β | 2018 | β |
| SignaLink: Multilayered Regulatory Networks. | Csabai L et al. | β | 2018 | β |
| Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. | Huang JK et al. | β | 2018 | β |
| TET1-Mediated Hypomethylation Activates Oncogenic Signaling in Triple-Negative Breast Cancer. | Good CR et al. | β | 2018 | β |
| The Fas Signaling Pathway Is a Common Genetic Risk Factor for Severe Cutaneous Drug Adverse Reactions Across Diverse Drugs. | Park HW et al. | β | 2018 | β |
| Transcriptomic responses to extreme low salinity among locally adapted populations of Olympia oyster (Ostrea lurida). | Maynard A et al. | β | 2018 | β |
| Unraveling endometriosis-associated ovarian carcinomas using integrative proteomics. | Leung F et al. | β | 2018 | β |
| Using set theory to reduce redundancy in pathway sets. | Stoney RA et al. | β | 2018 | β |
| A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. | Way GP et al. | β | 2017 | β |
| Characterizing the "POAGome": A bioinformatics-driven approach to primary open-angle glaucoma. | Danford ID et al. | β | 2017 | β |
| Colorectal cancer stages transcriptome analysis. | Huo T et al. | β | 2017 | β |
| Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. | Molineros JE et al. | β | 2017 | β |
| Connectome Disconnectivity and Cortical Gene Expression in Patients With Schizophrenia. | Romme IA et al. | β | 2017 | β |
| Cross-species gene modules emerge from a systems biology approach to osteoarthritis. | Mueller AJ et al. | β | 2017 | β |
| Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. | Wathieu H et al. | β | 2017 | β |
| DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. | Shadle SC et al. | β | 2017 | β |
| EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He Y et al. | β | 2017 | β |
| Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. | Polo A et al. | β | 2017 | β |
| Functional and prognostic significance of the genomic amplification of frizzled 6 (FZD6) in breast cancer. | Corda G et al. | β | 2017 | β |
| GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. | Chen S et al. | β | 2017 | β |
| Gene Expression Profiling in Human Lung Cells Exposed to Isoprene-Derived Secondary Organic Aerosol. | Lin YH et al. | β | 2017 | β |
| Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. | Brockmann M et al. | β | 2017 | β |
| Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. | Zuo Y et al. | β | 2017 | β |
| Inhibition of Ξ²-Glucocerebrosidase Activity Preserves Motor Unit Integrity in a Mouse Model of Amyotrophic Lateral Sclerosis. | Henriques A et al. | β | 2017 | β |
| Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets. | Riddell N et al. | β | 2017 | β |
| PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. | Gioutlakis A et al. | β | 2017 | β |
| Regulated Expansion and Survival of Chimeric Antigen Receptor-Modified T Cells Using Small Molecule-Dependent Inducible MyD88/CD40. | Foster AE et al. | β | 2017 | β |
| Remodeling of heterochromatin structure slows neuropathological progression and prolongs survival in an animal model of Huntington's disease. | Lee J et al. | β | 2017 | β |
| Requirement of Zinc Transporter SLC39A7/ZIP7 for Dermal Development to Fine-Tune Endoplasmic Reticulum Function by Regulating Protein Disulfide Isomerase. | Bin BH et al. | β | 2017 | β |
| Sphingolipid Metabolism Is Dysregulated at Transcriptomic and Metabolic Levels in the Spinal Cord of an Animal Model of Amyotrophic Lateral Sclerosis. | Henriques A et al. | β | 2017 | β |
| Transcriptomic Analysis of the Claudin Interactome in Malignant Pleural Mesothelioma: Evaluation of the Effect of Disease Phenotype, Asbestos Exposure, and CDKN2A Deletion Status. | Rouka E et al. | β | 2017 | β |
| Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic. | Evans TG et al. | β | 2017 | β |
| Tsc2 disruption in mesenchymal progenitors results in tumors with vascular anomalies overexpressing <i>Lgals3</i>. | Klover PJ et al. | β | 2017 | β |
| Unmasking Transcriptional Heterogeneity in Senescent Cells. | Hernandez-Segura A et al. | β | 2017 | β |
| VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in Genome-Wide Association Studies: applied to Alzheimer's Disease. | Liu Q et al. | β | 2017 | β |
| Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma. | Rieswijk L et al. | β | 2016 | β |
| Analyzing and interpreting genome data at the network level with ConsensusPathDB. | Herwig R et al. | β | 2016 | β |
| Aurora-A Kinase: A Potent Oncogene and Target for Cancer Therapy. | Yan M et al. | β | 2016 | β |
| Bidirectional Expression of Metabolic, Structural, and Immune Pathways in Early Myopia and Hyperopia. | Riddell N et al. | β | 2016 | β |
| Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. | Ma S et al. | β | 2016 | β |
| Chromosome 19 amplification correlates with advanced disease in adrenocortical carcinoma. | Rubinstein JC et al. | β | 2016 | β |
| Comparative analysis of protein interactome networks prioritizes candidate genes with cancer signatures. | Li Y et al. | β | 2016 | β |
| Deep sequencing of small RNA libraries from human prostate epithelial and stromal cells reveal distinct pattern of microRNAs primarily predicted to target growth factors. | Singh S et al. | β | 2016 | β |
| DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines. | Tian S et al. | β | 2016 | β |
| Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. | Huang CH et al. | β | 2016 | β |
| Ebola virus encodes a miR-155 analog to regulate importin-Ξ±5 expression. | Liu Y et al. | β | 2016 | β |
| Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB. | Beber ME et al. | β | 2016 | β |
| Efficient and Powerful Method for Combining P-Values in Genome-Wide Association Studies. | Vilor-Tejedor N et al. | β | 2016 | β |
| Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. | Poczobutt JM et al. | β | 2016 | β |
| Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. | Sun N et al. | β | 2016 | β |
| Gene expression profiling predicts pathways and genes associated with Parkinson's disease. | Liu S et al. | β | 2016 | β |
| Genetic and epigenetic methylation defects and implication of the ERMN gene in autism spectrum disorders. | Homs A et al. | β | 2016 | β |
| Identifying Significant Features in Cancer Methylation Data Using Gene Pathway Segmentation. | Hira ZM et al. | β | 2016 | β |
| Multivariate Genetic Correlates of the Auditory Paired Stimuli-Based P2 Event-Related Potential in the Psychosis Dimension From the BSNIP Study. | Mokhtari M et al. | β | 2016 | β |
| Network Approaches to the Understanding of Alzheimer's Disease: From Model Organisms to Humans. | Yerbury J et al. | β | 2016 | β |
| PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations. | Soul J et al. | β | 2016 | β |
| Proteomic Characterization of Exosomes from HIV-1-Infected Cells. | Li M et al. | β | 2016 | β |
| Proteomic profiling of epileptogenesis in a rat model: Focus on inflammation. | Walker A et al. | β | 2016 | β |
| Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer. | Xu L et al. | β | 2016 | β |
| RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method. | Zhao J et al. | β | 2016 | β |
| Shifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma. | Rubinstein JC et al. | β | 2016 | β |
| Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer. | Wu W et al. | β | 2016 | β |
| Transcriptional Profiling of Th2 Cells Identifies Pathogenic Features Associated with Asthma. | Seumois G et al. | β | 2016 | β |
| Transcriptional profiling revealed the anti-proliferative effect of MFN2 deficiency and identified risk factors in lung adenocarcinoma. | Lou Y et al. | β | 2016 | β |
| Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence. | Molinari E et al. | β | 2016 | β |
| Transcriptome Analysis of the Human Striatum in Tourette Syndrome. | Lennington JB et al. | β | 2016 | β |
| Characterization of Skin Aging-Associated Secreted Proteins (SAASP) Produced by Dermal Fibroblasts Isolated from Intrinsically Aged Human Skin. | Waldera Lupa DM et al. | β | 2015 | β |
| Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. | Chowdhury S et al. | β | 2015 | β |
| Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents. | Voisin S et al. | β | 2015 | β |
| Differential regulation of microRNAs in end-stage failing hearts is associated with left ventricular assist device unloading. | Barsanti C et al. | β | 2015 | β |
| Disentangling the multigenic and pleiotropic nature of molecular function. | Stoney RA et al. | β | 2015 | β |
| Distinct genotype-dependent differences in transcriptome responses in humans exposed to environmental carcinogens. | EspΓn-PΓ©rez A et al. | β | 2015 | β |
| DNA methylation abnormalities in congenital heart disease. | Serra-JuhΓ© C et al. | β | 2015 | β |
| Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes. | Rieswijk L et al. | β | 2015 | β |
| Global MicroRNA Analysis in Primary Hepatocyte Cultures. | Krauskopf J et al. | β | 2015 | β |
| Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. | Park JM et al. | β | 2015 | β |
| Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes. | Lukowski SW et al. | β | 2015 | β |
| Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes. | Lukowski SW et al. | β | 2015 | β |
| miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation. | Eedunuri VK et al. | β | 2015 | β |
| Network and systems biology: essential steps in virtualising drug discovery and development. | Wierling C et al. | β | 2015 | β |
| PathCards: multi-source consolidation of human biological pathways. | Belinky F et al. | β | 2015 | β |
| PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. | Soul J et al. | β | 2015 | β |
| Sex-specific molecular genetic response to UVB exposure in Xiphophorus maculatus skin. | Boswell W et al. | β | 2015 | β |
| Specific and redundant activities of ETV1 and ETV4 in prostate cancer aggressiveness revealed by co-overexpression cellular contexts. | Mesquita D et al. | β | 2015 | β |
| The gene expression profiling of hepatocellular carcinoma by a network analysis approach shows a dominance of intrinsically disordered proteins (IDPs) between hub nodes. | Singh S et al. | β | 2015 | β |
| Tools for visualization and analysis of molecular networks, pathways, and -omics data. | Villaveces JM et al. | β | 2015 | β |
| Using gene expression signatures to identify novel treatment strategies in gulf war illness. | Craddock TJ et al. | β | 2015 | β |
| Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. | Garmhausen M et al. | β | 2015 | β |
| Xanthophylls lutein and zeaxanthin modify gene expression and induce synthesis of hyaluronan in keratinocyte model of human skin. | Li R et al. | β | 2015 | β |
| A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. | Newton R et al. | β | 2014 | β |
| Drug repositioning discovery for early- and late-stage non-small-cell lung cancer. | Huang CH et al. | β | 2014 | β |
| Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. | Seumois G et al. | β | 2014 | β |
| Genome-wide analysis reveals DNA methylation markers that vary with both age and obesity. | AlmΓ©n MS et al. | β | 2014 | β |
| Gibbon genome and the fast karyotype evolution of small apes. | Carbone L et al. | β | 2014 | β |
| In silico identification of potential targets and drugs for non-small cell lung cancer. | Huang CH et al. | β | 2014 | β |
| Integrative cross-omics analysis in primary mouse hepatocytes unravels mechanisms of cyclosporin A-induced hepatotoxicity. | Van den Hof WF et al. | β | 2014 | β |
| Metabolic phenotyping and systems biology approaches to understanding metabolic syndrome and fatty liver disease. | Dumas ME et al. | β | 2014 | β |
| Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. | Aberg KA et al. | β | 2014 | β |
| Practical aspects of genome-wide association interaction analysis. | Gusareva ES et al. | β | 2014 | β |
| Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. | Waldera-Lupa DM et al. | β | 2014 | β |
| Radiosensitization of human leukemic HL-60 cells by ATR kinase inhibitor (VE-821): phosphoproteomic analysis. | Ε alovskΓ‘ B et al. | β | 2014 | β |
| A comprehensive family-based replication study of schizophrenia genes. | Aberg KA et al. | β | 2013 | β |
| A preliminary study of the whole-genome expression profile of sporadic and monogenic early-onset Alzheimer's disease. | Antonell A et al. | β | 2013 | β |
| LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells. | Fogeron ML et al. | β | 2013 | β |
| Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. | Cannistraci CV et al. | β | 2013 | β |
| TFII-I regulates target genes in the PI-3K and TGF-Ξ² signaling pathways through a novel DNA binding motif. | Segura-Puimedon M et al. | β | 2013 | β |
| The ConsensusPathDB interaction database: 2013 update. | Kamburov A et al. | β | 2013 | β |
| Time and dose-dependent effects of phenobarbital on the rat liver miRNAome. | Koufaris C et al. | β | 2013 | β |
| Using random walks to identify cancer-associated modules in expression data. | Petrochilos D et al. | β | 2013 | β |
| A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. | Jozefczuk J et al. | β | 2012 | β |
| Comparative interactomics with Funcoup 2.0. | Alexeyenko A et al. | β | 2012 | β |
| Contribution of rare copy number variants to isolated human malformations. | Serra-JuhΓ© C et al. | β | 2012 | β |
| DIPSBC--data integration platform for systems biology collaborations. | Dreher F et al. | β | 2012 | β |
| Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome. | McIntyre RE et al. | β | 2012 | β |
| Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. | Mora A et al. | β | 2012 | β |
| Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. | Demirkan A et al. | β | 2012 | β |
| Identification of androgen-regulated genes in human prostate. | Vaarala MH et al. | β | 2012 | β |
| IMID: integrated molecular interaction database. | Balaji S et al. | β | 2012 | β |
| Integrated analysis of gene copy number, copy neutral LOH, and microRNA profiles in adult acute lymphoblastic leukemia. | Ninomiya S et al. | β | 2012 | β |
| Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes. | Dumas ME | β | 2012 | β |
| PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. | Chen C et al. | β | 2012 | β |
| Public domain databases for medicinal chemistry. | Nicola G et al. | β | 2012 | β |
| A systems biological study on the comorbidity of autism spectrum disorders and bipolar disorder. | Ragunath P et al. | β | 2011 | β |
| CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. | Ahmed J et al. | β | 2011 | β |
| ConsensusPathDB: toward a more complete picture of cell biology. | Kamburov A et al. | β | 2011 | β |
| Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. | Cavill R et al. | β | 2011 | β |
| Critical assessment of human metabolic pathway databases: a stepping stone for future integration. | Stobbe MD et al. | β | 2011 | β |
| GIDMP: good protein-protein interaction data metamining practice. | Plewczynski D et al. | β | 2011 | β |
| High-throughput analyses and curation of protein interactions in yeast. | Wodak SJ et al. | β | 2011 | β |
| Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. | Goel R et al. | β | 2011 | β |
| Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients. | Porzelius C et al. | β | 2011 | β |
| Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes. | Vilardell M et al. | β | 2011 | β |
| PROMISCUOUS: a database for network-based drug-repositioning. | von Eichborn J et al. | β | 2011 | β |
| Proteomic patterns of cervical cancer cell lines, a network perspective. | Higareda-Almaraz JC et al. | β | 2011 | β |
| SPIKE: a database of highly curated human signaling pathways. | Paz A et al. | β | 2011 | β |
| Standards, tools, and databases for the analysis of yeast 'omics data. | Kowald A et al. | β | 2011 | β |
| Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development. | Lascorz J et al. | β | 2011 | β |
| The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. | Szklarczyk D et al. | β | 2011 | β |
| Comparative phenotypic assessment of cardiac pathology, physiology, and gene expression in C3H/HeJ, C57BL/6J, and B6C3F1/J mice. | Auerbach SS et al. | β | 2010 | β |
| Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry. | Hauck SM et al. | β | 2010 | β |
| Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. | Pentchev K et al. | β | 2010 | β |
| From NPC therapeutic target identification to potential treatment strategy. | Lan MY et al. | β | 2010 | β |
| Genome-wide association study for colorectal cancer identifies risk polymorphisms in German familial cases and implicates MAPK signalling pathways in disease susceptibility. | Lascorz J et al. | β | 2010 | β |
| Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. | Johannes M et al. | β | 2010 | β |
| iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. | Turner B et al. | β | 2010 | β |
| Literature curation of protein interactions: measuring agreement across major public databases. | Turinsky AL et al. | β | 2010 | β |
| MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. | Sucaet Y et al. | β | 2010 | β |
| Suppression of the transcription factor MSX1 gene delays bovine preimplantation embryo development in vitro. | Tesfaye D et al. | β | 2010 | β |
| Transcriptome profile in Williams-Beuren syndrome lymphoblast cells reveals gene pathways implicated in glucose intolerance and visuospatial construction deficits. | Antonell A et al. | β | 2010 | β |
| In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. | Chavez L et al. | β | 2009 | β |
| Neuroscience in the era of functional genomics and systems biology. | Geschwind DH et al. | β | 2009 | β |