Genomes and Genes
protein interaction maps
Summary: Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
- Lei L, Zhenzhong L, Lin L, Bo P. Uncovering the pathogenesis of microtia using bioinformatics approach. Int J Pediatr Otorhinolaryngol. 2017;99:30-35 pubmed publisher..And we also predicted that several potential mechanisms might contribute to occurrence of microtia by disturbing GO terms and pathways. This approach could be useful for the study of the etiology and pathogenesis of microtia. ..
- Bresciani A, Missineo A, Gallo M, Cerretani M, Fezzardi P, Tomei L, et al. Nuclear factor (erythroid-derived 2)-like 2 (NRF2) drug discovery: Biochemical toolbox to develop NRF2 activators by reversible binding of Kelch-like ECH-associated protein 1 (KEAP1). Arch Biochem Biophys. 2017;631:31-41 pubmed publisher
- Shafaghati L, Razaghi Moghadam Z, Mohammadnejad J. A Systems Biology Approach to Understanding Alcoholic Liver Disease Molecular Mechanism: The Development of Static and Dynamic Models. Bull Math Biol. 2017;79:2450-2473 pubmed publisher..The static network of ALD and its dynamic model are the first models provided for ALD which offer potentially valuable information for researchers in this field. ..
- . Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls. Am J Hum Genet. 2013;92:854-65 pubmed publisher..PINBPA is a powerful approach to gaining further insights into the biology of associated genes and to prioritizing candidates for subsequent genetic studies of complex traits. ..
- Ghadie M, Lambourne L, Vidal M, Xia Y. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PLoS Comput Biol. 2017;13:e1005717 pubmed publisher..Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing. ..
- Lavallée Adam M, Cloutier P, Coulombe B, Blanchette M. Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. Nucleic Acids Res. 2017;45:10415-10427 pubmed publisher..We validate in vivo the role in protein expression regulation of three motifs identified by LESMoN...
- Wang P, Yu X, Lü J. Identification and evolution of structurally dominant nodes in protein-protein interaction networks. IEEE Trans Biomed Circuits Syst. 2014;8:87-97 pubmed publisher..Our investigations shed some light on the future applications of the evolving characteristics of bio-molecular networks, such as reengineering of particular networks for technological, synthetic or pharmacological purposes. ..
- Xiong W, Liu H, Guan J, Zhou S. Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. BMC Bioinformatics. 2013;14 Suppl 12:S4 pubmed publisher..Furthermore, the experimental results also indicate that our method is significantly better than the compared approaches in sparsely-labeled networks, and it is robust to the change of the proportion of annotated proteins. ..
- Yasui T, Yamamoto T, Sakai N, Asano K, Takai T, Yoshitomi Y, et al. Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design. Bioorg Med Chem. 2017;25:4876-4886 pubmed publisher..72µM) by utilizing structure-based drug design (SBDD) based on an X-ray crystal structure of 1a bound to BCL6. Compound 8c also showed a good pharmacokinetic profile, which was acceptable for both in vitro and in vivo studies. ..
- Mertins B, Psakis G, Essen L. Voltage-dependent anion channels: the wizard of the mitochondrial outer membrane. Biol Chem. 2014;395:1435-42 pubmed publisher..Here we review recent progress in terms of VDACs' structure and regulation, with a special focus on the molecular aspects of gating and the interaction with effector proteins. ..
- Zhang N, Zhang Y, Zhao S, Sun Y. Septin4 as a novel binding partner of PARP1 contributes to oxidative stress induced human umbilical vein endothelial cells injure. Biochem Biophys Res Commun. 2018;496:621-627 pubmed publisher..In conclusions, our founding indicates that Septin4 is a novel essential factor involved in oxidative stress induced vascular endothelial cell injury by interacting with apoptosis-related protein PARP1. ..
- Han Z, Huang H, Gao Y, Huang Q. Functional annotation of Alzheimer's disease associated loci revealed by GWASs. PLoS ONE. 2017;12:e0179677 pubmed publisher..Our results provided the targets for further experimental assessment and further insight on AD pathophysiology. ..
- Karim M, Yoshizawa T, Sobuz S, Sato Y, Yamagata K. Sirtuin 7-dependent deacetylation of DDB1 regulates the expression of nuclear receptor TR4. Biochem Biophys Res Commun. 2017;490:423-428 pubmed publisher..Our results indicate that the SIRT7-mediated deacetylation of K1121 attenuates the activity of the CUL4B/DDB1/DCAF1 E3 ubiquitin ligase complex by reducing binding between DDB1 and DCAF1, leading to the increased expression of TR4. ..
- Sun J, Zhu K, Zheng W, Xu H. A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinformatics. 2015;16 Suppl 5:S1 pubmed publisher..The results provide some foundational network characteristics for further designing computational strategies to predict novel drug targets and drug repurposing. ..
- Scholtes S, Kramer E, Weisser M, Roth W, Luginbühl R, Grossner T, et al. Global chondrocyte gene expression after a single anabolic loading period: Time evolution and re-inducibility of mechano-responses. J Cell Physiol. 2018;233:699-711 pubmed publisher..Upregulation of mechanosensitive indicators extending differentially into the resting time provides crucial knowledge to maximize cartilage matrix deposition for the generation of high-level cartilage replacement tissue. ..
- Afonso M, de Lima L, Bleicher L. Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box. BMC Genomics. 2013;14 Suppl 6:S1 pubmed publisher..We conclude that DNA specificity and functional surface specialization has independently driven nuclear receptor evolution, and suggest possible binding modes for the class of divergent nuclear receptors in nematodes. ..
- Dohrmann J, Puchin J, Singh R. Global multiple protein-protein interaction network alignment by combining pairwise network alignments. BMC Bioinformatics. 2015;16 Suppl 13:S11 pubmed publisher..The speed, flexibility and the ability to retain prior correspondences as new networks are aligned, makes SMAL a compelling choice for alignment of multiple large networks. ..
- Yu F, Yang Z, Hu X, Sun Y, Lin H, Wang J. Protein complex detection in PPI networks based on data integration and supervised learning method. BMC Bioinformatics. 2015;16 Suppl 12:S3 pubmed publisher..In addition, our protein complexes detection method can achieve better performance than ClusterONE. ..
- Gazi M, Moharram S, MarhÃ¤ll A, Kazi J. The dual specificity PI3K/mTOR inhibitor PKI-587 displays efficacy against T-cell acute lymphoblastic leukemia (T-ALL). Cancer Lett. 2017;392:9-16 pubmed publisher..This preclinical study shows beneficial effects of PKI-587 on T-ALL that warrants further investigation in the clinical setting. ..
- Wu X, Ruan L, Yang Y, Mei Q. Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma. Biol Res. 2017;50:6 pubmed publisher..Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC. ..
- Tan X, Amran F, Thayan R, Ahmad N, Jaafar R, Haron R, et al. Potential serum biomarkers associated with mild and severe leptospirosis infection: A cohort study in the Malaysian population. Electrophoresis. 2017;38:2141-2149 pubmed publisher..In conclusion, this finding supports the potential of these five proteins to be the biomarkers for mild and severe human leptospirosis. ..
- Hanke M, Foraita R. Clone temporal centrality measures for incomplete sequences of graph snapshots. BMC Bioinformatics. 2017;18:261 pubmed publisher..The proposed REN algorithm allows to calculate (clone) temporal centrality measures even for long snapshot sequences. ..
- Ali N, Wu J, Hochgräfe F, Chan H, Nair R, Ye S, et al. Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways. Breast Cancer Res. 2014;16:437 pubmed publisher..The Met-amplified, p53-null tumours provide a new preclinical model for a subset of triple-negative breast cancers. ..
- Kaushik G, Thomas M, Aho K. Psychoactive pharmaceuticals as environmental contaminants may disrupt highly inter-connected nodes in an Autism-associated protein-protein interaction network. BMC Bioinformatics. 2015;16 Suppl 7:S3 pubmed publisher..The results indicate that important gene sets in the ASD network are particularly susceptible to perturbation by pharmaceuticals at environmental concentrations. ..
- Qin C, Sun Y, Dong Y. A new computational strategy for identifying essential proteins based on network topological properties and biological information. PLoS ONE. 2017;12:e0182031 pubmed publisher..In particular, our strategy improves the prediction accuracy to 89, 78, 79, and 85 percent on the YDIP, YMIPS, YMBD and YHQ datasets at the top 100 level, respectively. ..
- Gao B, Yu T, Xue D, Sun B, Shao Q, Choudhry H, et al. A multidimensional integration analysis reveals potential bridging targets in the process of colorectal cancer liver metastasis. PLoS ONE. 2017;12:e0178760 pubmed publisher..This study enhances our understanding of the genetic alterations and transcriptional regulation that drive the metastatic process, but also provides the methodology to guide the studies on other metastatic cancers. ..
- Sneha P, Thirumal Kumar D, Saini S, Kajal K, Magesh R, Siva R, et al. Analyzing the Effect of V66M Mutation in BDNF in Causing Mood Disorders: A Computational Approach. Adv Protein Chem Struct Biol. 2017;108:85-103 pubmed publisher..With the use of in silico tools and computational macroscopic methods, we identified a decrease in the alpha-helix nature, and an overall increase in the random coils that could have probably resulted in deformation of the protein. ..
- Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, et al. Genome-scale identification and characterization of moonlighting proteins. Biol Direct. 2014;9:30 pubmed publisher..This article was reviewed by Michael Galperin, Eugine Koonin, and Nick Grishin. ..
- Cantres Rosario Y, Acevedo Mariani F, Perez Laspiur J, Haskins W, Plaud M, Cantres Rosario Y, et al. Microwave & magnetic proteomics of macrophages from patients with HIV-associated cognitive impairment. PLoS ONE. 2017;12:e0181779 pubmed publisher..Further studies are warranted to determine if these proteins may be target candidates for therapy development against HACI. ..
- Wong Y, Wu C, Lai H, Jheng B, Weng H, Chang T, et al. Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data. BMC Syst Biol. 2015;9 Suppl 6:S4 pubmed publisher..We hope this work helps scientists reveal more hidden cellular mechanisms of stroke etiology and repair processes. ..
- Wang Q, Shi C, Lv S. Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways. Braz J Med Biol Res. 2017;50:e5981 pubmed publisher..Moreover, we found that these 30 pathways had crosstalks with each other. The results suggest that these dysregulated pathways might be used as biomarkers to diagnose CRC. ..
- Zhou C, Chen T, Xie Z, Qin Y, Ou Y, Zhang J, et al. RACK1 forms a complex with FGFR1 and PKM2, and stimulates the growth and migration of squamous lung cancer cells. Mol Carcinog. 2017;56:2391-2399 pubmed publisher..Taken together, our study demonstrated the pivotal roles of RACK1 in FGFR1/PKM2 signaling, suggesting FGFR1/RACK1/PKM2 might be a therapeutic target for lung cancer treatment. ..
- Sims R, van der Lee S, Naj A, Bellenguez C, Badarinarayan N, Jakobsdottir J, et al. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease. Nat Genet. 2017;49:1373-1384 pubmed publisher..These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease. ..
- Shi Z, Fujii K, Kovary K, Genuth N, Röst H, Teruel M, et al. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol Cell. 2017;67:71-83.e7 pubmed publisher..Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression. ..
- Li D, Pan Z, Hu G, Zhu Z, He S. Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme. BMC Genomics. 2017;18:209 pubmed publisher..The effectiveness of proposed algorithm is validated on both small and large protein interaction networks. ..
- QuirÃ³s P, Prado M, Zamboni N, D Amico D, Williams R, Finley D, et al. Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals. J Cell Biol. 2017;216:2027-2045 pubmed publisher..Our data illustrate the value of a multiomics approach to characterize complex cellular networks and provide a versatile resource to identify new regulators of mitochondrial-related diseases. ..
- Twarda Clapa A, Krzanik S, Kubica K, Guzik K, Labuzek B, Neochoritis C, et al. 1,4,5-Trisubstituted Imidazole-Based p53-MDM2/MDMX Antagonists with Aliphatic Linkers for Conjugation with Biological Carriers. J Med Chem. 2017;60:4234-4244 pubmed publisher..This unique dimerization-binding mode opens new prospects for the optimization of the p53-MDM2/MDMX inhibitors and conjugation with bioactive carriers. ..
- Teku G, Vihinen M. Simulation of the dynamics of primary immunodeficiencies in CD4+ T-cells. PLoS ONE. 2017;12:e0176500 pubmed publisher..The approach confirms previous knowledge about T-cell signaling network and indicates several new important proteins that may be of interest when developing novel diagnosis and therapies to treat immunological defects. ..
- Bastos P, Ferreira R, Manadas B, Moreira P, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci. 2017;54:185-204 pubmed publisher..The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases. ..
- Pan A, Lahiri C, Rajendiran A, Shanmugham B. Computational analysis of protein interaction networks for infectious diseases. Brief Bioinform. 2016;17:517-26 pubmed publisher..This would provide useful insights to the research community, thereby enabling them to design novel biomedicine against such infectious diseases. ..
- Galgano D, Onnis A, Pappalardo E, Galvagni F, Acuto O, Baldari C. The T cell IFT20 interactome reveals new players in immune synapse assembly. J Cell Sci. 2017;130:1110-1121 pubmed publisher..Our data underscore the traffic-related role of an IFT20 complex that includes components of the intracellular trafficking machinery in IS assembly. ..
- Elegheert J, Cvetkovska V, Clayton A, Heroven C, Vennekens K, Smukowski S, et al. Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins. Neuron. 2017;95:896-913.e10 pubmed publisher..These results illustrate a potentially brain-wide regulatory mechanism for NL-NRX signaling modulation. ..
- Martínez Gil L, Vera Velasco N, Mingarro I. Exploring the Human-Nipah Virus Protein-Protein Interactome. J Virol. 2017;91: pubmed publisher..Furthermore, our data present a large number of putative drug targets that could be exploited for the treatment of this infection. ..