R3BG8R last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

i2d
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

Other names: I2D, i2d

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

Webpage:

http://ophid.utoronto.ca/ophidv2.204/

Licence:

Name: other
URL: http://ophid.utoronto.ca/ophidv2.204/downloads.jsp

Publications:

Publications
More detailed information about this field from each metasource.

Online predicted human interaction database
PMID: 15657099
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

Unequal evolutionary conservation of human protein interactions in interologous networks
PMID: 17535438
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

Online predicted human interaction database PubMed citations: 260.

260 articles citing: Online predicted human interaction database

PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
Identification of kidney injury released circulating osteopontin as causal agent of respiratory failure. PMID:35213222
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action. PMID:34278363
Databases for Protein-Protein Interactions. PMID:34236665
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
scConnect: a method for exploratory analysis of cell-cell communication based on single cell RNA sequencing data. PMID:33974001
Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level. PMID:33841510
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Tumor cell endogenous HIF-1α activity induces aberrant angiogenesis and interacts with TRAF6 pathway required for colorectal cancer development. PMID:33142239
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. PMID:32841121
MICA enhances sensitivity to cisplatin in patients with extensive small cell lung cancer via downregulation of ABCG2. PMID:32724354
Network Systems Pharmacology-Based Mechanism Study on the Beneficial Effects of Vitamin D against Psychosis in Alzheimer's Disease. PMID:32273551
Applications of Network Pharmacology in Traditional Chinese Medicine Research. PMID:32148533
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Computer aided analysis of disease linked protein networks. PMID:31485137
Quantitative proteomic analysis of sperm in unexplained recurrent pregnancy loss. PMID:31288842
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets. PMID:31119214
Identifying mouse developmental essential genes using machine learning. PMID:30563825
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers. PMID:30413626
Network pharmacology-based strategy to investigate pharmacological mechanisms of Zuojinwan for treatment of gastritis. PMID:30382864
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
Computational characterization and identification of human polycystic ovary syndrome genes. PMID:30154492
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. PMID:29643987
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
The UCSC Genome Browser database: 2018 update. PMID:29106570
Main active constituent identification in Guanxinjing capsule, a traditional Chinese medicine, for the treatment of coronary heart disease complicated with depression. PMID:28858293
A network pharmacology-based strategy deciphers the underlying molecular mechanisms of Qixuehe Capsule in the treatment of menstrual disorders. PMID:28835770
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
On the performance of de novo pathway enrichment. PMID:28649433
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
Network-based characterization and prediction of human DNA repair genes and pathways. PMID:28368026
The essential and downstream common proteins of amyotrophic lateral sclerosis: A protein-protein interaction network analysis. PMID:28282387
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
The post-genomic era of biological network alignment. PMID:28194172
Network pharmacology-based identification of key pharmacological pathways of Yin-Huang-Qing-Fei capsule acting on chronic bronchitis. PMID:28053519
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. PMID:27756223
The epichaperome is an integrated chaperome network that facilitates tumour survival. PMID:27706135
Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications. PMID:27559342
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PMID:27380265
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Guizhi-Shaoyao-Zhimu decoction attenuates rheumatoid arthritis partially by reversing inflammation-immune system imbalance. PMID:27277474
MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. PMID:27267444
Revealing the Effects of the Herbal Pair of Euphorbia kansui and Glycyrrhiza on Hepatocellular Carcinoma Ascites with Integrating Network Target Analysis and Experimental Validation. PMID:27143956
Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma. PMID:27081085
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
Discovering distinct functional modules of specific cancer types using protein-protein interaction networks. PMID:26495282
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
STAT3 pathway regulates lung-derived brain metastasis initiating cell capacity through miR-21 activation. PMID:26314961
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
Systems biology of neurodegenerative diseases. PMID:26065845
A functional biological network centered on XRCC3: a new possible marker of chemoradiotherapy resistance in rectal cancer patients. PMID:26023803
A systematic investigation based on microRNA-mediated gene regulatory network reveals that dysregulation of microRNA-19a/Cyclin D1 axis confers an oncogenic potential and a worse prognosis in human hepatocellular carcinoma. PMID:25985117
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
Deciphering the pharmacological mechanism of the Chinese formula huanglian-jie-du decoction in the treatment of ischemic stroke using a systems biology-based strategy. PMID:25937634
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information. PMID:25870785
Disease gene prioritization using network and feature. PMID:25844670
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation. PMID:25820382
IIIDB: a database for isoform-isoform interactions and isoform network modules. PMID:25707505
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Kinome-wide screening of HER2+ breast cancer cells for molecules that mediate cell proliferation or sensitize cells to trastuzumab therapy. PMID:25500906
Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway. PMID:25424347
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. PMID:25364745
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
A systems biology-based approach to uncovering the molecular mechanisms underlying the effects of dragon's blood tablet in colitis, involving the integration of chemical analysis, ADME prediction, and network pharmacology. PMID:25068885
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Integrating genomics and proteomics data to predict drug effects using binary linear programming. PMID:25036040
Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker. PMID:25028927
Predicting disease-related proteins based on clique backbone in protein-protein interaction network. PMID:25013377
Hemolymph proteome changes during worker brood development match the biological divergences between western honey bees (Apis mellifera) and eastern honey bees (Apis cerana). PMID:24996860
Similar morphological and molecular signatures shared by female and male germline stem cells. PMID:24993338
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
A systems biology investigation of neurodegenerative dementia reveals a pivotal role of autophagy. PMID:24908109
In-depth proteomics characterization of embryogenesis of the honey bee worker (Apis mellifera ligustica). PMID:24895377
Ensemble positive unlabeled learning for disease gene identification. PMID:24816822
Modelling the yeast interactome. PMID:24589662
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma. PMID:24561634
Network analysis of neurodegenerative disease highlights a role of Toll-like receptor signaling. PMID:24551850
Review of biological network data and its applications. PMID:24465231
Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis? PMID:24403051
Identification of GRB2 and GAB1 coexpression as an unfavorable prognostic factor for hepatocellular carcinoma by a combination of expression profile and network analysis. PMID:24391994
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
An algorithm for network-based gene prioritization that encodes knowledge both in nodes and in links. PMID:24260251
Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PMID:24244318
Integrating in silico resources to map a signaling network. PMID:24233784
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Revealing the hidden relationship by sparse modules in complex networks with a large-scale analysis. PMID:23762457
A systems biology-based investigation into the pharmacological mechanisms of wu tou tang acting on rheumatoid arthritis by integrating network analysis. PMID:23690848
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas. PMID:23483937
Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners. PMID:23483542
Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. PMID:23476684
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Visual data mining of biological networks: one size does not fit all. PMID:23341759
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. PMID:23282181
Mining functional subgraphs from cancer protein-protein interaction networks. PMID:23282132
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. PMID:23281828
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Positive-unlabeled learning for disease gene identification. PMID:22923290
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Prioritizing cancer-related key miRNA-target interactions by integrative genomics. PMID:22705797
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
Identification of novel ATP13A2 interactors and their role in α-synuclein misfolding and toxicity. PMID:22645275
A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PMID:22558100
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. PMID:22548703
MOfinder: a novel algorithm for detecting overlapping modules from protein-protein interaction network. PMID:22500072
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
Bayesian Joint Modeling of Multiple Gene Networks and Diverse Genomic Data to Identify Target Genes of a Transcription Factor. PMID:22408712
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. PMID:22196356
BinTree seeking: a novel approach to mine both bi-sparse and cohesive modules in protein interaction networks. PMID:22140454
Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins. PMID:22136443
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis. PMID:22071792
Inferring pleiotropy by network analysis: linked diseases in the human PPI network. PMID:22034985
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
The general definition of the p97/valosin-containing protein (VCP)-interacting motif (VIM) delineates a new family of p97 cofactors. PMID:21896481
Stem cell gene expression programs influence clinical outcome in human leukemia. PMID:21873988
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Large-scale de novo prediction of physical protein-protein association. PMID:21836163
Molecular evolution of cyclin proteins in animals and fungi. PMID:21798004
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
Integrative computational biology for cancer research. PMID:21691773
PINTA: a web server for network-based gene prioritization from expression data. PMID:21602267
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
PRIN: a predicted rice interactome network. PMID:21575196
Characterizing the diversity and biological relevance of the MLPCN assay manifold and screening set. PMID:21568288
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
The role of indirect connections in gene networks in predicting function. PMID:21551147
Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer. PMID:21474781
Interleukin-1 receptor-mediated inflammation impairs the heat shock response of human mesothelial cells. PMID:21435443
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
Analysis of AML Genes in Dysregulated Molecular Networks. PMID:21347161
A GDI (AGS3) and a GEF (GIV) regulate autophagy by balancing G protein activity and growth factor signals. PMID:21209316
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. PMID:21190591
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
Functional genomics complements quantitative genetics in identifying disease-gene associations. PMID:21085640
Concept and application of a computational vaccinology workflow. PMID:21067549
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. PMID:21059271
Integrative analysis of -omics data and histologic scoring in renal disease and transplantation: renal histogenomics. PMID:21044763
Characterising and predicting haploinsufficiency in the human genome. PMID:20976243
Identification of high-quality cancer prognostic markers and metastasis network modules. PMID:20975711
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. PMID:20926419
Dynamic interaction networks in a hierarchically organized tissue. PMID:20924352
Finding the "dark matter" in human and yeast protein network prediction and modelling. PMID:20885791
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
The BioPAX community standard for pathway data sharing. PMID:20829833
Increased entropy of signal transduction in the cancer metastasis phenotype. PMID:20673354
A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. PMID:20670417
Inferring modules from human protein interactome classes. PMID:20653930
Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PMID:20585543
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. PMID:20576703
Response of the mosquito protein interaction network to dengue infection. PMID:20553610
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
The power of protein interaction networks for associating genes with diseases. PMID:20185403
Integrative approaches to the prediction of protein functions based on the feature selection. PMID:20043848
Network-based Identification of novel cancer genes. PMID:19959820
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. PMID:19850753
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. PMID:19837718
Analysis of AML genes in dysregulated molecular networks. PMID:19761572
Semantic similarity in biomedical ontologies. PMID:19649320
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PMID:19649302
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. PMID:19594875
Comparative analysis of protein-protein interactions in cancer-associated genes. PMID:19591789
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
Slit diaphragms contain tight junction proteins. PMID:19478094
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
Finding common protein interaction patterns across organisms. PMID:19455201
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
Cancer as a system failure. PMID:19390665
Biological process linkage networks. PMID:19390589
Microarray and bioinformatics analysis of gene expression in experimental membranous nephropathy. PMID:19390219
Connecting protein interaction data, mutations, and disease using bioinformatics. PMID:19381537
Tissue specificity and the human protein interaction network. PMID:19357639
A top-down approach to infer and compare domain-domain interactions across eight model organisms. PMID:19333396
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. PMID:19208173
Dynamic modularity in protein interaction networks predicts breast cancer outcome. PMID:19182785
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. PMID:19067583
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
PIPs: human protein-protein interaction prediction database. PMID:18988626
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. PMID:18984619
Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments. PMID:18949072
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
A genomewide functional network for the laboratory mouse. PMID:18818725
Interspecies data mining to predict novel ING-protein interactions in human. PMID:18801192
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. PMID:18793469
An en masse phenotype and function prediction system for Mus musculus. PMID:18613952
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. PMID:18613949
Predicting gene function in a hierarchical context with an ensemble of classifiers. PMID:18613947
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. PMID:18613946
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. PMID:18586725
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Network-based global inference of human disease genes. PMID:18463613
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. PMID:18424801
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
An integrated approach to inferring gene-disease associations in humans. PMID:18300252
A mixture of feature experts approach for protein-protein interaction prediction. PMID:18269700
Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: a systems biology perspective. PMID:18266955
Linking the ovarian cancer transcriptome and immunome. PMID:18173842
Gene regulatory networks in lactation: identification of global principles using bioinformatics. PMID:18039394
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. PMID:17916244
A predicted interactome for Arabidopsis. PMID:17675552
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
Characterization of protein-interaction networks in tumors. PMID:17597514
Evidence for systems-level molecular mechanisms of tumorigenesis. PMID:17584915
Functional coordination of alternative splicing in the mammalian central nervous system. PMID:17565696
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. PMID:17486137
UniHI: an entry gate to the human protein interactome. PMID:17158159
Analysis of protein sequence and interaction data for candidate disease gene prediction. PMID:17020920
Modelling protein-protein interaction networks via a stickiness index. PMID:16971339
Global topological features of cancer proteins in the human interactome. PMID:16844706
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. PMID:16603075
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. PMID:16188928
Unequal evolutionary conservation of human protein interactions in interologous networks PubMed citations: 137.

137 articles citing: Unequal evolutionary conservation of human protein interactions in interologous networks

What the protein data bank tells us about the evolutionary conservation of protein conformational diversity. PMID:35762711
Topsy-Turvy: integrating a global view into sequence-based PPI prediction. PMID:35758793
Integration of Protein-Protein Interaction Networks and Gene Expression Profiles Helps Detect Pancreatic Adenocarcinoma Candidate Genes. PMID:35711911
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Computational Network Inference for Bacterial Interactomics. PMID:35353009
Identification of kidney injury released circulating osteopontin as causal agent of respiratory failure. PMID:35213222
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models. PMID:34858485
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
HIV-Proteins-Associated CNS Neurotoxicity, Their Mediators, and Alternative Treatments. PMID:34562223
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. PMID:34255742
Databases for Protein-Protein Interactions. PMID:34236665
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PMID:33006999
Cell-Type-Specific Proteogenomic Signal Diffusion for Integrating Multi-Omics Data Predicts Novel Schizophrenia Risk Genes. PMID:32984858
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. PMID:32380953
A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins. PMID:32327964
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer. PMID:31440276
Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus. PMID:31319636
UBL4A inhibits autophagy-mediated proliferation and metastasis of pancreatic ductal adenocarcinoma via targeting LAMP1. PMID:31288830
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. PMID:29643987
Correlates of evolutionary rates in the murine sperm proteome. PMID:29580206
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships. PMID:29312990
THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. PMID:29157087
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. PMID:29028184
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
De novo pathway-based biomarker identification. PMID:28934488
Multidimensional integrative analysis uncovers driver candidates and biomarkers in penile carcinoma. PMID:28751665
Strength of functional signature correlates with effect size in autism. PMID:28687074
Properties of genes essential for mouse development. PMID:28562614
HABP2 p.G534E variant in patients with family history of thyroid and breast cancer. PMID:28402931
The essential and downstream common proteins of amyotrophic lateral sclerosis: A protein-protein interaction network analysis. PMID:28282387
The effects of shared information on semantic calculations in the gene ontology. PMID:28217262
The post-genomic era of biological network alignment. PMID:28194172
An Integrated Approach Identifies Mediators of Local Recurrence in Head and Neck Squamous Carcinoma. PMID:28174235
A network-based pathway-expanding approach for pathway analysis. PMID:28155638
A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. PMID:28065597
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
A computational interactome and functional annotation for the human proteome. PMID:27770567
The epichaperome is an integrated chaperome network that facilitates tumour survival. PMID:27706135
Robust de novo pathway enrichment with KeyPathwayMiner 5. PMID:27540470
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
Local versus global biological network alignment. PMID:27357169
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. PMID:27267444
KeyPathwayMinerWeb: online multi-omics network enrichment. PMID:27150809
Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma. PMID:27081085
A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. PMID:26777674
Fundamentals of protein interaction network mapping. PMID:26681426
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
STAT3 pathway regulates lung-derived brain metastasis initiating cell capacity through miR-21 activation. PMID:26314961
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Novel drug target identification for the treatment of dementia using multi-relational association mining. PMID:26154857
Integrative Analysis Reveals Regulatory Programs in Endometriosis. PMID:26134036
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
L-GRAAL: Lagrangian graphlet-based network aligner. PMID:25725498
Algorithmic approaches to protein-protein interaction site prediction. PMID:25713596
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
Kinome-wide screening of HER2+ breast cancer cells for molecules that mediate cell proliferation or sensitize cells to trastuzumab therapy. PMID:25500906
Conserved abundance and topological features in chromatin-remodeling protein interaction networks. PMID:25427557
In silico prediction of physical protein interactions and characterization of interactome orphans. PMID:25402006
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. PMID:25385592
A network-based classification model for deriving novel drug-disease associations and assessing their molecular actions. PMID:25356910
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
GeneMANIA: Fast gene network construction and function prediction for Cytoscape. PMID:25254104
PPI layouts: BioJS components for the display of Protein-Protein Interactions. PMID:25075288
Similar morphological and molecular signatures shared by female and male germline stem cells. PMID:24993338
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
In-depth proteomics characterization of embryogenesis of the honey bee worker (Apis mellifera ligustica). PMID:24895377
Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. PMID:24892934
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Prediction and redesign of protein-protein interactions. PMID:24878423
Comparison of reprogramming genes in induced pluripotent stem cells and nuclear transfer cloned embryos. PMID:24828831
Disordered proteinaceous machines. PMID:24702702
The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. PMID:24658140
Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis? PMID:24403051
An algorithm for network-based gene prioritization that encodes knowledge both in nodes and in links. PMID:24260251
Integrating in silico resources to map a signaling network. PMID:24233784
The diminishing role of hubs in dynamical processes on complex networks. PMID:24004558
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
SH3 interactome conserves general function over specific form. PMID:23549480
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
Visualization of protein interaction networks: problems and solutions. PMID:23368786
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
A methodology for detecting the orthology signal in a PPI network at a functional complex level. PMID:22759423
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
Genome-wide identification of palmitate-regulated immediate early genes and target genes in pancreatic beta-cells reveals a central role of NF-κB. PMID:22302392
Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. PMID:22196356
Automated microinjection of recombinant BCL-X into mouse zygotes enhances embryo development. PMID:21799744
Integrative computational biology for cancer research. PMID:21691773
PRIN: a predicted rice interactome network. PMID:21575196
Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. PMID:21526989
Cancer computational biology. PMID:21521513
Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer. PMID:21474781
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
A knowledge-based weighting framework to boost the power of genome-wide association studies. PMID:21217833
The role of exon shuffling in shaping protein-protein interaction networks. PMID:21210967
Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma. PMID:20831814
Measuring the physical cohesiveness of proteins using physical interaction enrichment. PMID:20798171
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. PMID:20513650
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma. PMID:20113529
Gene socialization: gene order, GC content and gene silencing in Salmonella. PMID:20003346
Elucidation of functional consequences of signalling pathway interactions. PMID:19895694
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. PMID:19850753
Integrating diverse information to gain more insight into microarray analysis. PMID:19834567
The emerging role of the RAB25 small GTPase in cancer. PMID:19719478
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
Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology. PMID:19536202
Slit diaphragms contain tight junction proteins. PMID:19478094
High throughput interaction data reveals degree conservation of hub proteins. PMID:19209717
Lung cancer: developmental networks gone awry? PMID:19202349
An evolutionary and structural characterization of mammalian protein complex organization. PMID:19108706
TAp73 knockout shows genomic instability with infertility and tumor suppressor functions. PMID:18805989
Interspecies data mining to predict novel ING-protein interactions in human. PMID:18801192

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More detailed information about this field from each metasource.

high-throughput screening
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

interologs mapping
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

network model
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

network simulation
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

signaling
metasource: Fairsharing.org
version: FAIRsharing.org: I2D; Interologous Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.k56rjs; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

hhv8
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

biological networks
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

fly
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

human
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

mouse
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

rat
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

worm
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

yeast
metasource: re3data.org
version: re3data.org: Interologous Interaction Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BG8R last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

protein interaction experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

high-throughput screening interologs mapping molecular interaction network model network simulation pathway model protein protein interaction signaling hhv8 biological networks fly human mouse rat worm yeast molecular interactions, pathways and networks protein interaction model organisms protein interaction experiment human

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I2D - Interologous Interaction Database

STRING

Integrated Interactions Database

ophid

Molecular INTeraction database

Biological General Repository for Interaction Datasets

HPID - Human Protein Interaction database

Bacterial Protein Interaction Database

DOMINE

Protein Interaction Network Analysis platform

DroID - Drosophila Interactions Database

Human Protein-Protein Interaction rEference

TRIP

PAIR

PSINDB

HitPredict

pathDIP

Microbial Protein Interaction Database

Yeast KID

AtPID