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.
- Makondi P, Chu C, Wei P, Chang Y. Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer. PLoS ONE. 2017;12:e0180616 pubmed publisher..Targeting the MAPK signal transduction pathway through the targeting of the FGF2, FGF9, MECOM, PLA2G4C and PRKACB might increase tumor responsiveness to irinotecan treatment. ..
- Lobingier B, Hüttenhain R, Eichel K, Miller K, Ting A, von Zastrow M, et al. An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell. 2017;169:350-360.e12 pubmed publisher..Validating its utility as a discovery pipeline, we establish that two of these proteins promote ubiquitin-linked receptor downregulation after prolonged activation. ..
- Sowmya G, Ranganathan S. Discrete structural features among interface residue-level classes. BMC Bioinformatics. 2015;16 Suppl 18:S8 pubmed publisher..These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs. ..
- Ivanov A, Gonzalez Pecchi V, Khuri L, Niu Q, Wang Y, Xu Y, et al. OncoPPi-informed discovery of mitogen-activated protein kinase kinase 3 as a novel binding partner of c-Myc. Oncogene. 2017;36:5852-5860 pubmed publisher..Together, the exploration of OncoPPi led to a new biological model in which MKK3 operates by two distinct mechanisms in cellular regulation through its phosphorylation of p38 and its activation of MYC through PPI. ..
- 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. ..
- 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...
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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, RÃ¶st 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. ..
- 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. ..