Pathway Commons
Names
More detailed information about this field from each metasource.
Pathway Commons
metasource: Fairsharing.org
version: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
PC
metasource: Fairsharing.org
version: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
pathway_commons
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
Names
More detailed information about this field from each metasource.
Pathway Commons
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
PC
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
pathway_commons
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
Other names: PC, pathway_commons
Names
More detailed information about this field from each metasource.
Pathway Commons
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
PC
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
pathway_commons
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.
Description
More detailed information about this field from each metasource.
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
Metabolic and signaling pathways from multiple organisms
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Collection of publicly available pathways from multiple organisms.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
Webpage:
http://www.pathwaycommons.orgWebpage
More detailed information about this field from each metasource.
http://www.pathwaycommons.org
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://www.pathwaycommons.org/
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
http://www.pathwaycommons.org/pc/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.pathwaycommons.org/pc/webservice.do?cmd=help
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
Licence:
Name: Public DomainLicence name
More detailed information about this field from each metasource.
Public Domain
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
http://www.pathwaycommons.org/
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
Pathway Commons, a web resource for biological pathway data
PMID: 21071392
metasource: Fairsharing.org
version: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://nar.oxfordjournals.org/content/39/suppl_1/D685
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkq1039
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
Publications
More detailed information about this field from each metasource.
Pathway Commons, a web resource for biological pathway data
PMID: 21071392
metasource: Fairsharing.org
version: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://nar.oxfordjournals.org/content/39/suppl_1/D685
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkq1039
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
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Pathway Commons, a web resource for biological pathway data
PubMed citations: 522.
522 articles citing: Pathway Commons, a web resource for biological pathway data
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Conserved Control Path in Multilayer Networks. PMID:35885201
Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. PMID:35740947
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. PMID:35737447
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes. PMID:35710749
Discrete modeling for integration and analysis of large-scale signaling networks. PMID:35696426
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization. PMID:35615022
Individualized discovery of rare cancer drivers in global network context. PMID:35593700
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Prioritizing Autism Risk Genes using Personalized Graphical Models Estimated from Single Cell RNA-seq Data. PMID:35529781
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PMID:35510183
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. PMID:35439941
Case Report: Exome and RNA Sequencing Identify a Novel de novo Missense Variant in HNRNPK in a Chinese Patient With Au-Kline Syndrome. PMID:35422839
Transcriptional Regulation of the Synaptic Vesicle Protein Synaptogyrin-3 (SYNGR3) Gene: The Effects of NURR1 on Its Expression. PMID:35409005
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Transcriptomics Reveals the Mevalonate and Cholesterol Pathways Blocking as Part of the Bacterial Cyclodipeptides Cytotoxic Effects in HeLa Cells of Human Cervix Adenocarcinoma. PMID:35359411
Application of Transcriptomics for Predicting Protein Interaction Networks, Drug Targets and Drug Candidates. PMID:35356062
Neurotrophic receptor tyrosine kinase family members in secretory and non-secretory breast carcinomas. PMID:35316931
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. PMID:35243422
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities. PMID:35186713
Novel epigenetic network biomarkers for early detection of esophageal cancer. PMID:35164838
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer. PMID:35035776
Abnormal sialylation and fucosylation of saliva glycoproteins: Characteristics of lung cancer-specific biomarkers. PMID:35005612
piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. PMID:34965192
Network-based cancer genomic data integration for pattern discovery. PMID:34886811
High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control. PMID:34845204
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
IL-27 Derived From Macrophages Facilitates IL-15 Production and T Cell Maintenance Following Allergic Hypersensitivity Responses. PMID:34659203
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
An overview of machine learning methods for monotherapy drug response prediction. PMID:34619752
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. PMID:34600580
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. PMID:34592927
The role of metadata in reproducible computational research. PMID:34553169
Revealing biomarkers associated with PARP inhibitors based on genetic interactions in cancer genome. PMID:34471490
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. PMID:34331449
Identification of genes associated with sudden cardiac death: a network- and pathway-based approach. PMID:34277054
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. PMID:34223192
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. PMID:34179843
Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction. PMID:34168265
Efficient representations of tumor diversity with paired DNA-RNA aberrations. PMID:34115745
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response. PMID:33992077
DNA Methylation and Expression Profiles of Whole Blood in Parkinson's Disease. PMID:33981329
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression. PMID:33963278
Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods. PMID:33946654
Statistical mechanics meets single-cell biology. PMID:33875884
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PMID:33861732
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. PMID:33835956
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. PMID:33683131
Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions. PMID:33670716
Bayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data. PMID:33664338
GeneWalk identifies relevant gene functions for a biological context using network representation learning. PMID:33526072
Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. PMID:33520715
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Large-scale regulatory and signaling network assembly through linked open data. PMID:33459761
Multiscale Regulation of the Intervertebral Disc: Achievements in Experimental, In Silico, and Regenerative Research. PMID:33445782
Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease. PMID:33441027
Prognostic Genetic Markers for Thrombosis in COVID-19 Patients: A Focused Analysis on D-Dimer, Homocysteine and Thromboembolism. PMID:33362545
Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. PMID:33333024
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data. PMID:33244588
Biliary-Atresia-Associated Mannosidase-1-Alpha-2 Gene Regulates Biliary and Ciliary Morphogenesis and Laterality. PMID:33192543
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
MCM2 and Carbonic Anhydrase 9 Are Novel Potential Targets for Neuroblastoma Pharmacological Treatment. PMID:33153038
Soluble Compounds Released by Hypoxic Stroma Confer Invasive Properties to Pancreatic Ductal Adenocarcinoma. PMID:33105540
CUEDC1 inhibits epithelial-mesenchymal transition via the TβRI/Smad signaling pathway and suppresses tumor progression in non-small cell lung cancer. PMID:33099540
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
A Genome-wide Association Study Discovers 46 Loci of the Human Metabolome in the Hispanic Community Health Study/Study of Latinos. PMID:33031748
Disease trajectory browser for exploring temporal, population-wide disease progression patterns in 7.2 million Danish patients. PMID:33009368
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. PMID:32995787
Identifying disease trajectories with predicate information from a knowledge graph. PMID:32819419
Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis. PMID:32732995
Footprint-based functional analysis of multiomic data. PMID:32685770
PEDL: extracting protein-protein associations using deep language models and distant supervision. PMID:32657389
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity. PMID:32355218
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. PMID:32326049
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. PMID:32196115
Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error. PMID:32193507
KCML: a machine-learning framework for inference of multi-scale gene functions from genetic perturbation screens. PMID:32141232
Integrative systems and functional analyses reveal a role of dopaminergic signaling in myelin pathogenesis. PMID:32122379
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PMID:32069277
Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer. PMID:32058975
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. PMID:31937236
TP63 isoform expression is linked with distinct clinical outcomes in cancer. PMID:31927310
Integrated analysis of gene modulation profile identifies pathogenic factors and pathways in the liver of diabetic mice. PMID:31890673
Interactive Multiresolution Visualization of Cellular Network Processes. PMID:31884165
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
Genetic links between endometriosis and cancers in women. PMID:31879572
Dynamically characterizing individual clinical change by the steady state of disease-associated pathway. PMID:31874621
Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis. PMID:31842970
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. PMID:31824580
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
Deep learning of pharmacogenomics resources: moving towards precision oncology. PMID:31813953
An omics perspective on drug target discovery platforms. PMID:31774113
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. PMID:31701125
Hypergraph-based connectivity measures for signaling pathway topologies. PMID:31652258
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. PMID:31631213
Advancing Pan-cancer Gene Expression Survial Analysis by Inclusion of Non-coding RNA. PMID:31607216
Single-cell transcriptomic profiling of the aging mouse brain. PMID:31551601
A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. PMID:31551593
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. PMID:31529053
Computer aided analysis of disease linked protein networks. PMID:31485137
Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations. PMID:31484939
Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes. PMID:31443155
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome. PMID:31428694
Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells. PMID:31400611
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. PMID:31365877
Big Data Approaches for Modeling Response and Resistance to Cancer Drugs. PMID:31342013
A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PMID:31335867
Somatic Alteration Burden Involving Non-Cancer Genes Predicts Prognosis in Early-Stage Non-Small Cell Lung Cancer. PMID:31330989
Data-driven characterization of molecular phenotypes across heterogeneous sample collections. PMID:31329928
Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers. PMID:31299925
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Cancer driver genes: a guilty by resemblance doctrine. PMID:31275738
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Label propagation defines signaling networks associated with recurrently mutated cancer genes. PMID:31253832
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways. PMID:31227749
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Effects of somatic alterations at pathway level are more mechanism-explanatory and clinically applicable to quantity of liver metastases of colorectal cancer. PMID:31219228
Altered Gene Expression of Thyroid Hormone Transporters and Deiodinases in iPS MeCP2-Knockout Cells-Derived Neurons. PMID:31214863
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
IgG based immunome analyses of breast cancer patients reveal underlying signaling pathways. PMID:31191821
The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. PMID:31133849
Optimal control nodes in disease-perturbed networks as targets for combination therapy. PMID:31097707
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Characterization of Glycolytic Enzymes and Pyruvate Kinase M2 in Type 1 and 2 Diabetic Nephropathy. PMID:31076418
INDRA-IPM: interactive pathway modeling using natural language with automated assembly. PMID:31070726
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
Identification, Quantification, and System Analysis of Protein N-ε Lysine Methylation in Anucleate Blood Platelets. PMID:30977292
Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders. PMID:30976086
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. PMID:30971826
Compositional epistasis detection using a few prototype disease models. PMID:30917131
Curating gene sets: challenges and opportunities for integrative analysis. PMID:30888410
Prognostic and Clinicopathological Significance of SERTAD1 in Various Types of Cancer Risk: A Systematic Review and Retrospective Analysis. PMID:30857225
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. PMID:30803482
A two-gene epigenetic signature for the prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer patients. PMID:30786922
Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches. PMID:30785707
Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. PMID:30723492
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. PMID:30696696
A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations. PMID:30670742
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. PMID:30624606
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
The BioGRID interaction database: 2019 update. PMID:30476227
Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a. PMID:30397325
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes. PMID:30341297
Using set theory to reduce redundancy in pathway sets. PMID:30340461
Typing tumors using pathways selected by somatic evolution. PMID:30297789
Computational identification and analysis of neurodegenerative disease associated protein kinases in hominid genomes. PMID:30258892
The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. PMID:30253781
Erianin inhibits human cervical cancer cell through regulation of tumor protein p53 via the extracellular signal-regulated kinase signaling pathway. PMID:30250566
A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target. PMID:30177815
A DNA-Methylated Sight on Autoimmune Inflammation Network across RA, pSS, and SLE. PMID:30159339
Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. PMID:30139811
A New Strategy to Uncover the Anticancer Mechanism of Chinese Compound Formula by Integrating Systems Pharmacology and Bioinformatics. PMID:30108661
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population. PMID:30081434
Differentially expressed genes related to major depressive disorder and antidepressant response: genome-wide gene expression analysis. PMID:30076325
INBIA: a boosting methodology for proteomic network inference. PMID:30066650
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. PMID:30066633
CIGene: a literature-based online resource for cancer initiation genes. PMID:30045691
Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach. PMID:29973620
Time Dependent Pathway Activation of Signalling Cascades in Rat Organs after Short-Term Hyperoxia. PMID:29973540
Inference of patient-specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer. PMID:29971923
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. PMID:29954318
Classifying tumors by supervised network propagation. PMID:29949979
Mega-analysis of Odds Ratio: A Convergent Method for a Deep Understanding of the Genetic Evidence in Schizophrenia. PMID:29931221
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. PMID:29921600
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. PMID:29893885
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. PMID:29872544
Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification. PMID:29869179
A comparison of mechanistic signaling pathway activity analysis methods. PMID:29868818
The Role of Systems Biologic Approach in Cell Signaling and Drug Development Responses-A Mini Review. PMID:29848999
Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network. PMID:29799522
Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. PMID:29789295
Cancer driver mutation prediction through Bayesian integration of multi-omic data. PMID:29738578
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich. PMID:29713020
Signalling maps in cancer research: construction and data analysis. PMID:29688383
YummyData: providing high-quality open life science data. PMID:29688370
Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach. PMID:29657291
Oncogenic Signaling Pathways in The Cancer Genome Atlas. PMID:29625050
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
SPV: a JavaScript Signaling Pathway Visualizer. PMID:29590303
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. PMID:29536824
Expression of TDRD9 in a subset of lung carcinomas by CpG island hypomethylation protects from DNA damage. PMID:29515758
Genetic heterogeneity of primary lesion and metastasis in small intestine neuroendocrine tumors. PMID:29491456
Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. PMID:29487189
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. PMID:29470400
Differential gene expression induced by anti-cancer agent plumbagin is mediated by androgen receptor in prostate cancer cells. PMID:29426892
Platelet procoagulant phenotype is modulated by a p38-MK2 axis that regulates RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis. PMID:29412690
A computationally driven analysis of the polyphenol-protein interactome. PMID:29396566
A Landscape of Metabolic Variation across Tumor Types. PMID:29396322
How the evolution of multicellularity set the stage for cancer. PMID:29337961
Easy and efficient ensemble gene set testing with EGSEA. PMID:29333246
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
Sirtuin 1-Chromatin-Binding Dynamics Points to a Common Mechanism Regulating Inflammatory Targets in SIV Infection and in the Aging Brain. PMID:29280055
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. PMID:29272327
Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis. PMID:29262532
Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. PMID:29250165
Prophetic Granger Causality to infer gene regulatory networks. PMID:29211761
Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer. PMID:29207666
Reactome diagram viewer: data structures and strategies to boost performance. PMID:29186351
Restoration of miR-29b exerts anti-cancer effects on glioblastoma. PMID:29176935
From word models to executable models of signaling networks using automated assembly. PMID:29175850
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
Reactome enhanced pathway visualization. PMID:29077811
CR2Cancer: a database for chromatin regulators in human cancer. PMID:29036683
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
An individualized gene expression signature for prediction of lung adenocarcinoma metastases. PMID:28922552
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis. PMID:28717649
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PMID:28650955
Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis. PMID:28617818
Contextualization of drug-mediator relations using evidence networks. PMID:28617226
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. PMID:28569836
Serum depletion induces changes in protein expression in the trophoblast-derived cell line HTR-8/SVneo. PMID:28536624
Identifying biologically relevant putative mechanisms in a given phenotype comparison. PMID:28486531
Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. PMID:28484005
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
Systematic analysis of gene expression alterations and clinical outcomes of adenylate cyclase-associated protein in cancer. PMID:28423713
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. PMID:28415074
Gene Network Reconstruction using Global-Local Shrinkage Priors. PMID:28408966
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Exome sequencing identified rare variants in genes HSPG2 and ATP2B4 in a family segregating developmental dysplasia of the hip. PMID:28327142
Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PMID:28306714
Proteome and Protein Network Analyses of Memory T Cells Find Altered Translation and Cell Stress Signaling in Treated Human Immunodeficiency Virus Patients Exhibiting Poor CD4 Recovery. PMID:28293663
Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury. PMID:28271248
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. PMID:28266149
SND1 acts as a novel gene transcription activator recognizing the conserved Motif domains of Smad promoters, inducing TGFβ1 response and breast cancer metastasis. PMID:28263968
Proteome Changes Induced by Imatinib and Novel Imatinib Derivatives in K562 Human Chronic Myeloid Leukemia Cells. PMID:28250386
Decreased Tissue COX5B Expression and Mitochondrial Dysfunction during Sepsis-Induced Kidney Injury in Rats. PMID:28246552
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach. PMID:28148498
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
The BioGRID interaction database: 2017 update. PMID:27980099
XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits. PMID:27964755
Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes. PMID:27929028
Epigenetic and genetic deregulation in cancer target distinct signaling pathway domains. PMID:27899617
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. PMID:27899558
OmniPath: guidelines and gateway for literature-curated signaling pathway resources. PMID:27898060
Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. PMID:27888226
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways. PMID:27832067
Meta-analysis of gene expression studies in endometrial cancer identifies gene expression profiles associated with aggressive disease and patient outcome. PMID:27830726
Proteomics profiling of interactome dynamics by colocalisation analysis (COLA). PMID:27824369
IDICAP: A Novel Tool for Integrating Drug Intervention Based on Cancer Panel. PMID:27801815
Approaches to modernize the combination drug development paradigm. PMID:27793177
Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice. PMID:27788253
The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development. PMID:27784795
Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data. PMID:27774993
Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments. PMID:27673562
In silico analysis of the transportome in human pancreatic ductal adenocarcinoma. PMID:27652669
LPRP: A Gene-Gene Interaction Network Construction Algorithm and Its Application in Breast Cancer Data Analysis. PMID:27640171
A Cytokine Signalling Network for the Regulation of Inducible Nitric Oxide Synthase Expression in Rheumatoid Arthritis. PMID:27626941
Analyzing and interpreting genome data at the network level with ConsensusPathDB. PMID:27606777
Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study. PMID:27556634
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes. PMID:27477450
Human Prostate Cancer Hallmarks Map. PMID:27476486
Trisomy 21 consistently activates the interferon response. PMID:27472900
In-silico interaction-resolution pathway activity quantification and application to identifying cancer subtypes. PMID:27455040
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid. PMID:27357110
Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance. PMID:27345421
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. PMID:27275538
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis. PMID:27239044
Functional/activity network (FAN) analysis of gene-phenotype connectivity liaised by grape polyphenol resveratrol. PMID:27232943
Nonoverlapping Clinical and Mutational Patterns in Melanomas from the Female Genital Tract and Atypical Genital Nevi. PMID:27220476
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Towards finding the linkage between metabolic and age-related disorders using semantic gene data network analysis. PMID:27212841
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery. PMID:27170263
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. PMID:27158457
Temporal Dysynchrony in brain connectivity gene expression following hypoxia. PMID:27146468
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets. PMID:27107567
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Expression of epithelial-mesenchymal transition-related genes increases with copy number in multiple cancer types. PMID:27029057
Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach. PMID:27004716
Transcriptional networks of murine diabetic peripheral neuropathy and nephropathy: common and distinct gene expression patterns. PMID:27000313
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
Pathway-Based Genomics Prediction using Generalized Elastic Net. PMID:26960204
Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. PMID:26947069
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PMID:26928298
Inferring causal molecular networks: empirical assessment through a community-based effort. PMID:26901648
Probabilistic Modeling of Imaging, Genetics and Diagnosis. PMID:26886973
Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone. PMID:26799318
Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types. PMID:26792175
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Pathway Analysis: State of the Art. PMID:26733877
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
HitWalker2: visual analytics for precision medicine and beyond. PMID:26708334
ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. PMID:26699919
PaxtoolsR: pathway analysis in R using Pathway Commons. PMID:26685306
Taking Bioinformatics to Systems Medicine. PMID:26677177
The integrative epigenomic-transcriptomic landscape of ER positive breast cancer. PMID:26664652
GeneWeaver: data driven alignment of cross-species genomics in biology and disease. PMID:26656951
Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data. PMID:26632845
NDEx, the Network Data Exchange. PMID:26594663
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. PMID:26590405
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Combined Genome-Wide CSF Aβ-42's Associations and Simple Network Properties Highlight New Risk Factors for Alzheimer's Disease. PMID:26576771
Nanomolar Caffeic Acid Decreases Glucose Uptake and the Effects of High Glucose in Endothelial Cells. PMID:26544184
Stroma-Derived Connective Tissue Growth Factor Maintains Cell Cycle Progression and Repopulation Activity of Hematopoietic Stem Cells In Vitro. PMID:26527384
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Phenotypic changes in the brain of SIV-infected macaques exposed to methamphetamine parallel macrophage activation patterns induced by the common gamma-chain cytokine system. PMID:26441851
Dynamical modeling of uncertain interaction-based genomic networks. PMID:26423606
DAPPER: a data-mining resource for protein-protein interactions. PMID:26405458
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. PMID:26400039
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. PMID:26374070
An algorithm for automated layout of process description maps drawn in SBGN. PMID:26363029
Extended LineSets: a visualization technique for the interactive inspection of biological pathways. PMID:26361500
PathwayMatrix: visualizing binary relationships between proteins in biological pathways. PMID:26361499
Data integration in biological research: an overview. PMID:26336651
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. PMID:26301688
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types. PMID:26292924
Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. PMID:26284497
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. PMID:26192618
Anatomy of BioJS, an open source community for the life sciences. PMID:26153621
Evolutionary trends and functional anatomy of the human expanded autophagy network. PMID:26103419
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
AMP-Activated Protein Kinase Interacts with the Peroxisome Proliferator-Activated Receptor Delta to Induce Genes Affecting Fatty Acid Oxidation in Human Macrophages. PMID:26098914
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PMID:26083494
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
Gene set analysis: A step-by-step guide. PMID:26059482
Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PMID:26058016
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes. PMID:26055097
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. PMID:26050742
Context-based resolution of semantic conflicts in biological pathways. PMID:26045143
Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. PMID:26029238
A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS. PMID:25984253
Extensive decoupling of metabolic genes in cancer. PMID:25961905
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. PMID:25956356
Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. PMID:25953855
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
Identification of sample-specific regulations using integrative network level analysis. PMID:25928379
Increased signaling entropy in cancer requires the scale-free property of protein interaction networks. PMID:25919796
Origin of cells and network information. PMID:25914760
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. PMID:25887147
Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study. PMID:25852169
IL-4Rα-dependent alternative activation of macrophages is not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice. PMID:25790379
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PMID:25790137
PathCards: multi-source consolidation of human biological pathways. PMID:25725062
Biological databases for human research. PMID:25712261
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Network representations of immune system complexity. PMID:25625853
Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors. PMID:25592566
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. PMID:25571995
β-Catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. PMID:25551153
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis. PMID:25522158
Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. PMID:25476789
Single-cell and multivariate approaches in genetic perturbation screens. PMID:25446316
The era of integrative genomics: more data or better methods? PMID:25431938
The BioGRID interaction database: 2015 update. PMID:25428363
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. PMID:25385592
Current advances in systems and integrative biology. PMID:25379142
Identifying common components across biological network graphs using a bipartite data model. PMID:25374613
Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer. PMID:25335771
EpilepsyGene: a genetic resource for genes and mutations related to epilepsy. PMID:25324312
Comparative network analysis via differential graphlet communities. PMID:25283527
Predicting interactome network perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia. PMID:25273558
In-vivo fusion of human cancer and hamster stromal cells permanently transduces and transcribes human DNA. PMID:25259521
Network medicine analysis of COPD multimorbidities. PMID:25248857
Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. PMID:25213708
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development. PMID:25191221
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
Network biology in medicine and beyond. PMID:25140061
Pathological brain plasticity and cognition in the offspring of males subjected to postnatal traumatic stress. PMID:25092246
Integrating biological pathways and genomic profiles with ChiBE 2. PMID:25086704
DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier. PMID:25079327
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Annotation of functional variation within non-MHC MS susceptibility loci through bioinformatics analysis. PMID:25030428
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. PMID:25015989
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
Comparison of REST cistromes across human cell types reveals common and context-specific functions. PMID:24922058
GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks. PMID:24911103
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
Biomarker gene signature discovery integrating network knowledge. PMID:24832044
Inference and validation of predictive gene networks from biomedical literature and gene expression data. PMID:24691108
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. PMID:24665131
Systems-level analysis of innate immunity. PMID:24655298
Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. PMID:24635915
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Synthetic lethal screens as a means to understand and treat MYC-driven cancers. PMID:24591535
JAK2-centered interactome hotspot identified by an integrative network algorithm in acute Stanford type A aortic dissection. PMID:24586754
A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments. PMID:24566931
Pathway-based drug repositioning using causal inference. PMID:24564553
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
Bias tradeoffs in the creation and analysis of protein-protein interaction networks. PMID:24480284
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. PMID:24336226
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
Pathway Commons at virtual cell: use of pathway data for mathematical modeling. PMID:24273241
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. PMID:24239728
Integrating in silico resources to map a signaling network. PMID:24233784
Protein kinase C epsilon and genetic networks in osteosarcoma metastasis. PMID:24216982
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
SMMRNA: a database of small molecule modulators of RNA. PMID:24163098
Cellular network entropy as the energy potential in Waddington's differentiation landscape. PMID:24154593
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PMID:24098138
Predicting functional gene interactions with the hierarchical interaction score. PMID:24097268
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Comprehensive identification of mutational cancer driver genes across 12 tumor types. PMID:24084849
Using biological pathway data with paxtools. PMID:24068901
Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. PMID:24065146
Pattern search in BioPAX models. PMID:24045775
Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. PMID:24039561
Network-based stratification of tumor mutations. PMID:24037242
Network and data integration for biomarker signature discovery via network smoothed T-statistics. PMID:24019896
Analyzing LC/MS metabolic profiling data in the context of existing metabolic networks. PMID:24010053
Incorporating prior knowledge into Gene Network Study. PMID:23956306
Mining large-scale response networks reveals 'topmost activities' in Mycobacterium tuberculosis infection. PMID:23892477
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. PMID:23880963
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources. PMID:23826291
iBIG: an integrative network tool for supporting human disease mechanism studies. PMID:23809576
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
PiHelper: an open source framework for drug-target and antibody-target data. PMID:23766416
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. PMID:23703215
The mutational landscape of adenoid cystic carcinoma. PMID:23685749
Steiner tree methods for optimal sub-network identification: an empirical study. PMID:23627667
Systematic curation of protein and genetic interaction data for computable biology. PMID:23587305
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. PMID:23568264
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. PMID:23550210
Identification of cancer fusion drivers using network fusion centrality. PMID:23505294
A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. PMID:23464878
A systems biology starter kit for arenaviruses. PMID:23342371
StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PMID:23284744
Discovering pathway cross-talks based on functional relations between pathways. PMID:23282018
Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PMID:23226239
The BioGRID interaction database: 2013 update. PMID:23203989
Logic modeling and the ridiculome under the rug. PMID:23171629
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Differential network entropy reveals cancer system hallmarks. PMID:23150773
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
Pathway Distiller - multisource biological pathway consolidation. PMID:23134636
A travel guide to Cytoscape plugins. PMID:23132118
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. PMID:23079107
TSGene: a web resource for tumor suppressor genes. PMID:23066107
A pathway-based classification of breast cancer integrating data on differentially expressed genes, copy number variations and microRNA target genes. PMID:22983731
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines. PMID:22912678
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Integrating literature-constrained and data-driven inference of signalling networks. PMID:22734019
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
Interferon-beta-1b-induced short- and long-term signatures of treatment activity in multiple sclerosis. PMID:22711062
The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. PMID:22641035
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. PMID:22588877
Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. PMID:22548963
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. PMID:22548703
Searching for cellular partners of hantaviral nonstructural protein NSs: Y2H screening of mouse cDNA library and analysis of cellular interactome. PMID:22506017
Bayesian integration of networks without gold standards. PMID:22492647
Omics and therapy - a basis for precision medicine. PMID:22445068
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
Identifying gene interaction networks. PMID:22307715
graphite - a Bioconductor package to convert pathway topology to gene network. PMID:22292714
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Mining and integration of pathway diagrams from imaging data. PMID:22267504
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PMID:22241976
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
Comparative interactomics with Funcoup 2.0. PMID:22110034
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. PMID:22096235
WikiPathways: building research communities on biological pathways. PMID:22096230
Databases and bioinformatics tools for the study of DNA repair. PMID:22091405
Software for systems biology: from tools to integrated platforms. PMID:22048662
Network based consensus gene signatures for biomarker discovery in breast cancer. PMID:22046239
NIRF constitutes a nodal point in the cell cycle network and is a candidate tumor suppressor. PMID:21952639
Mutual exclusivity analysis identifies oncogenic network modules. PMID:21908773
Integrative computational biology for cancer research. PMID:21691773
A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data. PMID:21612662
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PMID:21494657
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Regulation of alternative splicing by the core spliceosomal machinery. PMID:21325135 - http://nar.oxfordjournals.org/content/39/suppl_1/D685
- http://dx.doi.org/10.1093/nar/gkq1039
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More detailed information about this field from each metasource.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
dna
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
rna
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
biochemistry
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
cell-to-cell communication
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genetic interations
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genetics
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecular interactions
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecules
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
protein
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
proteomics
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
signaling pathways
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
system biology
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
systems biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:35.518182
Tags
More detailed information about this field from each metasource.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: PC; Pathway Commons; DOI: https://doi.org/10.25504/FAIRsharing.5y3gdd; Last edited: April 26, 2021, 11:37 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
dna
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
rna
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
biochemistry
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
cell-to-cell communication
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genetic interations
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genetics
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecular interactions
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecules
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
protein
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
proteomics
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
signaling pathways
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
system biology
metasource: re3data.orgversion: re3data.org: Pathway Commons; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3080J last accessed: 2022-11-04
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
systems biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:35.518182
pathway model metabolic and signaling pathways metabolic and signaling pathways dna rna biochemistry cell-to-cell communication genetic interations genetics genomics molecular interactions molecules protein proteomics signaling pathways system biology molecular interactions, pathways and networks systems biology
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