FunCoup 3.0: database of genome-wide functional coupling networks

scientific article published on 31 October 2013

FunCoup 3.0: database of genome-wide functional coupling networks is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/nar/SchmittOS14
P356DOI10.1093/NAR/GKT984
P932PMC publication ID3965084
P698PubMed publication ID24185702
P5875ResearchGate publication ID258253833

P50authorChristoph OgrisQ58203145
Erik SonnhammerQ30303525
P2093author name stringThomas Schmitt
P2860cites workA probabilistic functional network of yeast genesQ81067438
Computational identification of potential molecular interactions in ArabidopsisQ84207340
IsoRankN: spectral methods for global alignment of multiple protein networksQ37206322
Exploring the human genome with functional mapsQ37222777
CORUM: the comprehensive resource of mammalian protein complexes--2009Q38377952
Large-scale de novo prediction of physical protein-protein associationQ39451999
Predicting protein function by genomic context: quantitative evaluation and qualitative inferencesQ40414366
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interfaceQ41582682
Automatic parameter learning for multiple local network alignmentQ42237550
jSquid: a Java applet for graphical on-line network explorationQ46182522
Systematic computational prediction of protein interaction networksQ47581125
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes.Q48425002
NetworkBLAST: comparative analysis of protein networks.Q51897368
A user's guide to the encyclopedia of DNA elements (ENCODE)Q21092716
iRefIndex: a consolidated protein interaction database with provenanceQ21093638
The IntAct molecular interaction database in 2012Q24621004
InParanoid 7: new algorithms and tools for eukaryotic orthology analysisQ24643054
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene functionQ24646439
STRING: a database of predicted functional associations between proteinsQ24681946
CYGD: the Comprehensive Yeast Genome DatabaseQ24794671
Predicting functional gene links from phylogenetic-statistical analyses of whole genomesQ24811440
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectQ28301622
Assigning protein functions by comparative genome analysis: Protein phylogenetic profilesQ29039336
KEGG for integration and interpretation of large-scale molecular data setsQ29547277
Comparative assessment of large-scale data sets of protein-protein interactionsQ29547451
STRING v9.1: protein-protein interaction networks, with increased coverage and integrationQ29614691
Architecture of the human regulatory network derived from ENCODE dataQ29617046
Update on activities at the Universal Protein Resource (UniProt) in 2013Q29617361
Identification of functional elements and regulatory circuits by Drosophila modENCODEQ29617551
Proteomics. Integrating interactomesQ31034567
An improved method for identifying functionally linked proteins using phylogenetic profilesQ33287743
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiaeQ33301341
InParanoid 6: eukaryotic ortholog clusters with inparalogsQ33308437
Global networks of functional coupling in eukaryotes from comprehensive data integrationQ33412986
Network-based Identification of novel cancer genesQ33812883
Prioritizing candidate disease genes by network-based boosting of genome-wide association data.Q33887815
Comparative interactomics with Funcoup 2.0.Q34081235
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.Q34363843
Suppression of Myc oncogenic activity by nucleostemin haploinsufficiencyQ36016372
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networksQ36088404
Gene Ontology annotations and resourcesQ36491209
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P433issueDatabase issue
P407language of work or nameEnglishQ1860
P921main subjectdatabaseQ8513
P304page(s)D380-8
P577publication date2013-10-31
P1433published inNucleic Acids ResearchQ135122
P1476titleFunCoup 3.0: database of genome-wide functional coupling networks
P478volume42

Reverse relations

cites work (P2860)
Q93172647A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases
Q33823011A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications
Q38434459A large-scale benchmark of gene prioritization methods
Q92624635A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered pathways
Q42320854A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation
Q34524369APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
Q26774595Application of computational methods in genetic study of inflammatory bowel disease
Q28083558Applications of comparative evolution to human disease genetics
Q64109607Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms
Q58802595Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It
Q55620630CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency.
Q35979329CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations
Q30869228COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
Q39286993Characterization of potential driver mutations involved in human breast cancer by computational approaches
Q36086751Circulating proteins in response to combined-modality therapy in rectal cancer identified by antibody array screening
Q57859236Comparative Genomics Approaches to Identifying Functionally Related Genes
Q38564156Computational analysis of protein interaction networks for infectious diseases.
Q89686128Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder
Q52308820Determining the minimum number of protein-protein interactions required to support known protein complexes.
Q86818465Did we learn something new on pemphigoid autoimmune blistering diseases?
Q91650431Disease gene prediction for molecularly uncharacterized diseases
Q36933775Divergence in gene expression within and between two closely related flycatcher species
Q36820795Environmental Correlation Analysis for Genes Associated with Protection against Malaria
Q37721689Extracellular Vesicles Mediate Radiation-Induced Systemic Bystander Signals in the Bone Marrow and Spleen
Q35810193FNTM: a server for predicting functional networks of tissues in mouse
Q35810206FlyNet: a versatile network prioritization server for the Drosophila community
Q46256163FunCoup 4: new species, data, and visualization
Q55001949FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.
Q40749030Functional association networks as priors for gene regulatory network inference
Q47115723Gene gravity-like algorithm for disease gene prediction based on phenotype-specific network.
Q38823733Global profiling of protein complexes: current approaches and their perspective in biomedical research.
Q34427951HOX genes and their role in the development of human cancers.
Q35810319IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Q43215045InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
Q99714216Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma
Q31150071LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering.
Q28602218Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions
Q51084127MaxLink: network-based prioritization of genes tightly linked to a disease seed set.
Q38460161Molecular disease presentation in diabetic nephropathy.
Q47318797Molecular targets and signaling pathways regulated by nuclear translocation of syndecan-1.
Q36434721MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.
Q36236090Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family
Q36123583NEAT: an efficient network enrichment analysis test.
Q31056803PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data
Q39790343PathwAX: a web server for network crosstalk based pathway annotation
Q98725984Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
Q35705899Rare variants at 16p11.2 are associated with common variable immunodeficiency
Q30368859Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.
Q41714466Roles of sigma-1 receptors on mitochondrial functions relevant to neurodegenerative diseases
Q47849319S100A16 is a prognostic marker for colorectal cancer.
Q29615545STRING v10: protein-protein interaction networks, integrated over the tree of life
Q38370899Spatially resolved transcriptome profiling in model plant species
Q34217647Systematic transcriptome analysis of the zebrafish model of diamond-blackfan anemia induced by RPS24 deficiency
Q50973291The Role of Sigma-1 Receptor, an Intracellular Chaperone in Neurodegenerative Diseases.
Q39125771The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible
Q34675713The Sigma-1 Receptor as a Pluripotent Modulator in Living Systems.
Q35605573The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications
Q36264145The integration of weighted human gene association networks based on link prediction
Q30872328Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms
Q35951882Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia
Q47132768Upregulation of homeobox gene is correlated with poor survival outcomes in cervical cancer.
Q92121677Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks
Q90714042WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data
Q60044856When pitch adds to volume: coregulation of transcript diversity predicts gene function

Search more.