Interolog Regulog Database
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.
Description
More detailed information about this field from each metasource.
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
Webpage:
http://interolog.gersteinlab.org/Webpage
More detailed information about this field from each metasource.
http://interolog.gersteinlab.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
Publications:
Publications
More detailed information about this field from each metasource.
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
PMID: 15173116
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
Publications
More detailed information about this field from each metasource.
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
PMID: 15173116
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
PubMed citations: 222.
222 articles citing: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes. PMID:34683335
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
Databases for Protein-Protein Interactions. PMID:34236665
Prediction of Human-Plasmodium vivax Protein Associations From Heterogeneous Network Structures Based on Machine-Learning Approach. PMID:34188457
Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis. PMID:34093501
Ten Years of Collaborative Progress in the Quest for Orthologs. PMID:33822172
Within- and cross-species predictions of plant specialized metabolism genes using transfer learning. PMID:33344884
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
PtdIns4P restriction by hydrolase SAC1 decides specific fusion of autophagosomes with lysosomes. PMID:32693712
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. PMID:32380953
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Prediction of human-virus protein-protein interactions through a sequence embedding-based machine learning method. PMID:31969974
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome. PMID:31599923
Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats. PMID:31333643
Membrane protein-regulated networks across human cancers. PMID:31311925
Allopolyploid origin in Rubus (Rosaceae) inferred from nuclear granule-bound starch synthase I (GBSSI) sequences. PMID:31291892
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Construction and analysis of an interologous protein-protein interaction network of Camellia sinensis leaf (TeaLIPIN) from RNA-Seq data sets. PMID:31197449
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis. PMID:30755155
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
HumanNet v2: human gene networks for disease research. PMID:30418591
Genomic data integration systematically biases interactome mapping. PMID:30332399
In silico-prediction of protein-protein interactions network about MAPKs and PP2Cs reveals a novel docking site variants in Brachypodium distachyon. PMID:30305661
Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data. PMID:30166569
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
SWISS-MODEL: homology modelling of protein structures and complexes. PMID:29788355
The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. PMID:29666630
Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling. PMID:29348603
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Computational Analysis of Host-Pathogen Protein Interactions between Humans and Different Strains of Enterohemorrhagic Escherichia coli. PMID:28469995
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions. PMID:28365721
Transcriptome analysis reveals common differential and global gene expression profiles in bluetongue virus serotype 16 (BTV-16) infected peripheral blood mononuclear cells (PBMCs) in sheep and goats. PMID:28003963
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. PMID:27896959
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. PMID:27814699
Assessment of transfer methods for comparative genomics of regulatory networks in bacteria. PMID:27586594
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes. PMID:26766575
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
Fundamentals of protein interaction network mapping. PMID:26681426
Computational prediction of protein interfaces: A review of data driven methods. PMID:26460190
Panorama of ancient metazoan macromolecular complexes. PMID:26344197
The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment. PMID:25928711
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. PMID:25827022
Module organization and variance in protein-protein interaction networks. PMID:25797237
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. PMID:25739925
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
Text mining in cancer gene and pathway prioritization. PMID:25392685
Using biological networks to improve our understanding of infectious diseases. PMID:25379138
Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. PMID:25350354
OrthoClust: an orthology-based network framework for clustering data across multiple species. PMID:25249401
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. PMID:24953126
Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. PMID:24892934
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. PMID:24884676
Protein flexibility facilitates quaternary structure assembly and evolution. PMID:24866000
In silico prediction of protein-protein interactions in human macrophages. PMID:24636261
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
ppiPre: predicting protein-protein interactions by combining heterogeneous features. PMID:24565177
Computational large-scale mapping of protein-protein interactions using structural complexes. PMID:24510594
Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. PMID:24260261
Integrative approaches for finding modular structure in biological networks. PMID:24045689
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Computational analysis of virus-host interactomes. PMID:23996253
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
JiffyNet: a web-based instant protein network modeler for newly sequenced species. PMID:23685435
Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. PMID:23663963
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. PMID:23661758
Current challenges and future potential of tomato breeding using omics approaches. PMID:23641179
The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees. PMID:23620730
SH3 interactome conserves general function over specific form. PMID:23549480
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Computational prediction of protein-protein interactions in Leishmania predicted proteomes. PMID:23251492
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PMID:23209392
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Modeling dynamic regulatory processes in stroke. PMID:23071432
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase. PMID:22898364
Alternative protein-protein interfaces are frequent exceptions. PMID:22876170
Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PMID:22848637
Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PMID:22848443
Studying protein complexes by the yeast two-hybrid system. PMID:22841565
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. PMID:22750305
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. PMID:22688816
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. PMID:22595003
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Functional organization and its implication in evolution of the human protein-protein interaction network. PMID:22530615
Designing orthogonal signaling pathways: how to fit in with the surroundings. PMID:22451928
Network evolution: rewiring and signatures of conservation in signaling. PMID:22438796
PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. PMID:22419782
Homology inference of protein-protein interactions via conserved binding sites. PMID:22303436
Differential network biology. PMID:22252388
Evolution of biological interaction networks: from models to real data. PMID:22204388
Conserved BK channel-protein interactions reveal signals relevant to cell death and survival. PMID:22174833
Dissecting phosphorylation networks: lessons learned from yeast. PMID:22087660
A phenome-based functional analysis of transcription factors in the cereal head blight fungus, Fusarium graminearum. PMID:22028654
Biological interaction networks are conserved at the module level. PMID:21861884
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. PMID:21572178
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Supervised learning and prediction of physical interactions between human and HIV proteins. PMID:21382517
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. PMID:21257609
Measuring the evolutionary rewiring of biological networks. PMID:21253555
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789
Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction. PMID:21124869
Conserved and variable correlated mutations in the plant MADS protein network. PMID:20979667
Integrative systems biology and networks in autophagy. PMID:20842363
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. PMID:20807838
Measuring the physical cohesiveness of proteins using physical interaction enrichment. PMID:20798171
The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PMID:20711500
On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks. PMID:20699275
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. PMID:20513650
PCFamily: a web server for searching homologous protein complexes. PMID:20511590
Getting started in gene orthology and functional analysis. PMID:20361041
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Evolution of protein binding modes in homooligomers. PMID:19879880
Accounting for redundancy when integrating gene interaction databases. PMID:19847299
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. PMID:19843613
The Modular Organization of Protein Interactions in Escherichia coli. PMID:19798435
Evolutionarily conserved herpesviral protein interaction networks. PMID:19730696
The functional domain grouping of microtubule associated proteins. PMID:19704789
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms. PMID:19607657
Evolutionary flexibility of protein complexes. PMID:19583842
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Systems approach to explore components and interactions in the presynapse. PMID:19562802
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. PMID:19531251
Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners. PMID:19523227
IsoRankN: spectral methods for global alignment of multiple protein networks. PMID:19477996
Prediction of protein-protein interactions on the basis of evolutionary conservation of protein functions. PMID:19461979
Finding common protein interaction patterns across organisms. PMID:19455201
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. PMID:19356244
A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. PMID:19342671
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
Literature-curated protein interaction datasets. PMID:19116613
Regulation by transcription factors in bacteria: beyond description. PMID:19076632
Prediction of evolutionarily conserved interologs in Mus musculus. PMID:18842131
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. PMID:18820292
Transcriptional autoregulatory loops are highly conserved in vertebrate evolution. PMID:18791639
High-quality binary protein interaction map of the yeast interactome network. PMID:18719252
Conservation and topology of protein interaction networks under duplication-divergence evolution. PMID:18632555
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. PMID:18613946
Revisiting the Saccharomyces cerevisiae predicted ORFeome. PMID:18502943
Sequence-based prediction of protein-protein interactions by means of codon usage. PMID:18501006
Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system. PMID:18474041
Efficiency of the immunome protein interaction network increases during evolution. PMID:18430195
Predicting co-complexed protein pairs from heterogeneous data. PMID:18421371
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. PMID:18387196
Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. PMID:17997970
Host pathogen protein interactions predicted by comparative modeling. PMID:17965183
CORUM: the comprehensive resource of mammalian protein complexes. PMID:17965090
Bacteriome.org--an integrated protein interaction database for E. coli. PMID:17942431
Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum. PMID:17941702
A global analysis of genetic interactions in Caenorhabditis elegans. PMID:17897480
A predicted interactome for Arabidopsis. PMID:17675552
Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli. PMID:17617412
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Evidence for systems-level molecular mechanisms of tumorigenesis. PMID:17584915
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. PMID:17493288
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. PMID:17449655
Evolution of protein complexes by duplication of homomeric interactions. PMID:17411433
Specificity and evolvability in eukaryotic protein interaction networks. PMID:17305419
Transcriptional regulation of protein complexes within and across species. PMID:17227853
Evolutionary conservation of domain-domain interactions. PMID:17184549
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. PMID:17112386
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PMID:17054397
Comparison of protein interaction networks reveals species conservation and divergence. PMID:17044912
A direct comparison of protein interaction confidence assignment schemes. PMID:16872496
Protein-protein interactions more conserved within species than across species. PMID:16854211
Bacterial regulatory networks are extremely flexible in evolution. PMID:16840530
Protein complex compositions predicted by structural similarity. PMID:16738133
Differential evolutionary conservation of motif modes in the yeast protein interaction network. PMID:16638125
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. PMID:16606443
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. PMID:16603075
Protein interaction networks in plants. PMID:16575597
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. PMID:16434444
MPact: the MIPS protein interaction resource on yeast. PMID:16381906
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
The Plasmodium protein network diverges from those of other eukaryotes. PMID:16267557
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization. PMID:16209721
Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis. PMID:16192647
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PMID:16110343
Assessing the limits of genomic data integration for predicting protein networks. PMID:15998909
Genomes, phylogeny, and evolutionary systems biology. PMID:15851668
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Conserved patterns of protein interaction in multiple species. PMID:15687504
The Genomes of Oryza sativa: a history of duplications. PMID:15685292
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. PMID:15604458
A Drosophila protein-interaction map centered on cell-cycle regulators. PMID:15575970
Conservation and evolution of cis-regulatory systems in ascomycete fungi. PMID:15534694
Tags:
Tags
More detailed information about this field from each metasource.
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
protein interaction experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.554297
Tags
More detailed information about this field from each metasource.
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
protein interaction experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:08.554297
protein interaction molecular interactions, pathways and networks protein interaction experiment proteins
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