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Network protein function prediction

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https://www.readbyqxmd.com/read/28919414/changes-in-related-circular-rnas-following-er%C3%AE-knockdown-and-the-relationship-to-rbmsc-osteogenesis
#1
Xiaoyun Li, Bojia Peng, Xiaofeng Zhu, Panpan Wang, Yingquan Xiong, Hengrui Liu, Kehuan Sun, Haixia Wang, Ling Ou, Zhidi Wu, Xiaoguang Liu, Haibin He, Shu Mo, Xunqian Peng, Ya Tian, Ronghua Zhang, Li Yang
Recently, several studies have indicated that circular RNAs (circRNAs) play significant roles in various disease; however, Little is known about the chronology of estrogen receptor beta (ERβ) deficiency and altered circRNA expression, or their relationship with osteogenesis. Herein, we show through western-blot and quantitative real-time PCR assays, that when ERβ is silenced, the expression of osteogenesis-related proteins and mRNAs were down-regulated. We then performed RNA-Seq to analyze differential circRNA expression between the control and ERβ knockdown group...
September 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28919164/integrated-analysis-of-microrna-and-gene-expression-profiles-reveals-a-functional-regulatory-module-associated-with-liver-fibrosis
#2
Wei Chen, Wenshan Zhao, Aiting Yang, Anjian Xu, Huan Wang, Min Cong, Tianhui Liu, Ping Wang, Hong You
BACKGROUND: Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation have important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS: The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28919162/mir-101-1-expression-pattern-in-qinchuan-cattle-and-its-role-in-the-regulation-of-cell-differentiation
#3
Jiyao Wu, Dandan He, Binglin Yue, Chunlei Zhang, Xingtang Fang, Hong Chen
MiRNAs have emerged as key regulators of skeletal muscle development, but the knowledge of miRNAs in the molecular network of muscle development remains poorly understood. In this study, we designed to examine the biological function of bovine-miR-101-1. The bovine miR-101-1 was detected in the skeletal muscle of fetal, calf and adult cattle. Its abundance was significantly higher in the skeletal muscle of calf cattle than that in fetal and adult cattle. In the course of C2C12 myoblast differentiation, the expression of miR-101-1 gradually increased...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28912564/transcriptome-analysis-of-developing-lens-reveals-abundance-of-novel-transcripts-and-extensive-splicing-alterations
#4
Rajneesh Srivastava, Gungor Budak, Soma Dash, Salil A Lachke, Sarath Chandra Janga
Lens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. We show that the extent of novelty of expressed transcripts decreases significantly in post-natal lens compared to embryonic stages. Characterization of novel transcripts into partially novel transcripts (PNTs) and completely novel transcripts (CNTs) (novelty score ≥ 70%) revealed that the PNTs are both highly conserved across vertebrates and highly expressed across multiple stages...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904993/abnormalities-of-signal-transduction-networks-in-chronic-schizophrenia
#5
Jennifer L McGuire, Erica A Depasquale, Adam J Funk, Sinead M O'Donnovan, Kathryn Hasselfeld, Shruti Marwaha, John H Hammond, Vahram Hartounian, James H Meador-Woodruff, Jarek Meller, Robert E McCullumsmith
Schizophrenia is a serious neuropsychiatric disorder characterized by disruptions of brain cell metabolism, microstructure, and neurotransmission. All of these processes require coordination of multiple kinase-mediated signaling events. We hypothesize that imbalances in kinase activity propagate through an interconnected network of intracellular signaling with potential to simultaneously contribute to many or all of the observed deficits in schizophrenia. We established a workflow distinguishing schizophrenia-altered kinases in anterior cingulate cortex using a previously published kinome array data set...
2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28902459/exome-sequences-of-multiplex-multigenerational-families-reveal-schizophrenia-risk-loci-with-potential-implications-for-neurocognitive-performance
#6
Mark Z Kos, Melanie A Carless, Juan Peralta, Joanne E Curran, Ellen E Quillen, Marcio Almeida, August Blackburn, Lucy Blondell, David R Roalf, Michael F Pogue-Geile, Ruben C Gur, Harald H H Göring, Vishwajit L Nimgaonkar, Raquel E Gur, Laura Almasy
Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28901494/molecular-mechanisms-of-pathogenesis-in-hepatocellular-carcinoma-revealed-by-rna%C3%A2-sequencing
#7
Yao Liu, Zhe Yang, Feng Du, Qiao Yang, Jie Hou, Xiaohong Yan, Yi Geng, Yaning Zhao, Hua Wang
The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28900297/screening-candidate-microrna-mrna-regulatory-pairs-for-predicting-the-response-to-chemoradiotherapy-in-rectal-cancer-by-a-bioinformatics-approach
#8
Qiliang Peng, Junjia Zhu, Peipei Shen, Wenyan Yao, Yu Lei, Li Zou, Yingying Xu, Yuntian Shen, Yaqun Zhu
Extensive efforts have been undertaken in search of biomarkers for predicting the chemoradiotherapy response in rectal cancer. However, most attention on treatment efficiency prediction in carcinoma is addicted to single or limited molecules. Network biomarkers are considered to outperform single molecules in predictive power. In this study, candidate microRNAs (miRNAs) were identified from the PubMed citations and miRNA expression profiles. Targets of miRNAs were obtained from four experimentally confirmed interactions and three computationally predicted databases...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900113/abnormalities-of-signal-transduction-networks-in-chronic-schizophrenia
#9
Jennifer L McGuire, Erica A Depasquale, Adam J Funk, Sinead M O'Donnovan, Kathryn Hasselfeld, Shruti Marwaha, John H Hammond, Vahram Hartounian, James H Meador-Woodruff, Jarek Meller, Robert E McCullumsmith
Schizophrenia is a serious neuropsychiatric disorder characterized by disruptions of brain cell metabolism, microstructure, and neurotransmission. All of these processes require coordination of multiple kinase-mediated signaling events. We hypothesize that imbalances in kinase activity propagate through an interconnected network of intracellular signaling with potential to simultaneously contribute to many or all of the observed deficits in schizophrenia. We established a workflow distinguishing schizophrenia-altered kinases in anterior cingulate cortex using a previously published kinome array data set...
September 12, 2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28898928/importance-of-the-second-extracellular-loop-for-melatonin-mt1-receptor-function-and-absence-of-melatonin-binding-in-gpr50
#10
Nathalie Clement, Nicolas Renault, Jean-Luc Guillaume, Erika Cecon, Anne-Sophie Journé, Xavier Laurent, Kenjiro Tadagaki, Francis Cogé, Arnaud Gohier, Philippe Delagrange, Philippe Chavatte, Ralf Jockers
BACKGROUND AND PURPOSE: Recent crystal structures of G protein-coupled receptors (GPCRs) highlight the previously unappreciated role of the 2(nd) extracellular (E2) loop in ligand binding and gating and receptor activation. Here we studied the role of the E2 loop in the activation of the melatonin MT1 receptor (MT1 ) and in the inactivation of the closely related orphan GPR50 receptor. EXPERIMENTAL APPROACH: Chimeric MT1 -GPR50 receptors were generated and analyzed for 2-[(125) I]iodomelatonin binding, Gi /cAMP signaling and β-arrestin 2 recruitment assisted by computational molecular dynamics (MD) simulations...
September 12, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28894971/identification-of-genes-associated-with-primary-open-angle-glaucoma-by-bioinformatics-approach
#11
Haiyan Qiu, Benhu Zhu, Shengrong Ni
PURPOSE: This study aimed to identify associated genes with primary open-angle glaucoma (POAG) and explore the potentially modular mechanism underlying POAG. METHODS: We downloaded gene expression profiles data GSE27276 from gene expression omnibus and identified differentially expressed genes between POAG patients and normal controls. Then, gene ontology analysis and kyoto encyclopedia of genes and genomes pathway enrichment were performed to predict the DEGs functions, followed with the construction, centrality analysis, and module mining of protein-protein interaction network...
September 11, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28894115/in-silico-prediction-of-drug-target-interaction-networks-based-on-drug-chemical-structure-and-protein-sequences
#12
Zhengwei Li, Pengyong Han, Zhu-Hong You, Xiao Li, Yusen Zhang, Haiquan Yu, Ru Nie, Xing Chen
Analysis of drug-target interactions (DTIs) is of great importance in developing new drug candidates for known protein targets or discovering new targets for old drugs. However, the experimental approaches for identifying DTIs are expensive, laborious and challenging. In this study, we report a novel computational method for predicting DTIs using the highly discriminative information of drug-target interactions and our newly developed discriminative vector machine (DVM) classifier. More specifically, each target protein sequence is transformed as the position-specific scoring matrix (PSSM), in which the evolutionary information is retained; then the local binary pattern (LBP) operator is used to calculate the LBP histogram descriptor...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28889796/protein-protein-interaction-ppi-network-recent-advances-in-drug-discovery
#13
Alexiou Athanasios, Vairaktarakis Charalampos, Tsiamis Vasileios, Ghulam Md Ashraf
BACKGROUND: The investigation of the cellular components, their interactions and related functions constitute the major conditions in order to understand the cell as an integrated system. More specifically, the Protein-Protein Interactions and the obtained networks are very important in the majority of biological functions and processes, while most of the proteins appear to activate their functionalities through their interaction. METHODS: Our in depth review analysis, include Sixty-five peer-reviewed research and review studies from several bibliographic databases...
2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28881986/predicting-multicellular-function-through-multi-layer-tissue-networks
#14
Marinka Zitnik, Jure Leskovec
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here, we present OhmNet , a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28879530/correlation-analyses-revealed-global-microrna-mrna-expression-associations-in-human-peripheral-blood-mononuclear-cells
#15
Lan Wang, Jiang Zhu, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Xiao-Wei Zhu, Wei Xia, Fang-Fei Xie, Pei He, Peng-Fei Bing, Ying-Hua Qiu, Xiang Lin, Xin Lu, Lei Zhang, Neng-Jun Yi, Yong-Hong Zhang, Shu-Feng Lei
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28878621/the-networks-of-genes-encoding-palmitoylated-proteins-in-axonal-and-synaptic-compartments-are-affected-in-ppt1-overexpressing-neuronal-like-cells
#16
Francesco Pezzini, Marzia Bianchi, Salvatore Benfatto, Francesca Griggio, Stefano Doccini, Rosalba Carrozzo, Arvydas Dapkunas, Massimo Delledonne, Filippo M Santorelli, Maciej M Lalowski, Alessandro Simonati
CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 expression is also linked to synaptic compartments. The aim of this study was to unravel molecular signatures connected to CLN1. We utilized SH-SY5Y neuroblastoma cells overexpressing wild type CLN1 (SH-p.wtCLN1) and five selected CLN1 patients' mutations...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28878201/protein-complexes-prediction-method-based-on-core-attachment-structure-and-functional-annotations
#17
Bo Li, Bo Liao
Recent advances in high-throughput laboratory techniques captured large-scale protein-protein interaction (PPI) data, making it possible to create a detailed map of protein interaction networks, and thus enable us to detect protein complexes from these PPI networks. However, most of the current state-of-the-art studies still have some problems, for instance, incapability of identifying overlapping clusters, without considering the inherent organization within protein complexes, and overlooking the biological meaning of complexes...
September 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28874839/the-schistosoma-mansoni-genome-encodes-thousands-of-long-non-coding-rnas-predicted-to-be-functional-at-different-parasite-life-cycle-stages
#18
Elton J R Vasconcelos, Lucas F daSilva, David S Pires, Guilherme M Lavezzo, Adriana S A Pereira, Murilo S Amaral, Sergio Verjovski-Almeida
Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries)...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28874452/model-organisms-facilitate-rare-disease-diagnosis-and-therapeutic-research
#19
REVIEW
Michael F Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Jennifer E Posey, Monte Westerfield, John Postlethwait, Philip Hieter, Kym M Boycott, Philippe M Campeau, Hugo J Bellen
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions...
September 2017: Genetics
https://www.readbyqxmd.com/read/28873655/proteomic-analysis-of-sweet-algerian-apricot-kernels-prunus-armeniaca-l-by-combinatorial-peptide-ligand-libraries-and-lc-ms-ms
#20
Hamida Ghorab, Carmen Lammi, Anna Arnoldi, Zahia Kabouche, Gilda Aiello
An investigation on the proteome of the sweet kernel of apricot, based on equalisation with combinatorial peptide ligand libraries (CPLLs), SDS-PAGE, nLC-ESI-MS/MS, and database search, permitted identifying 175 proteins. Gene ontology analysis indicated that their main molecular functions are in nucleotide binding (20.9%), hydrolase activities (10.6%), kinase activities (7%), and catalytic activity (5.6%). A protein-protein association network analysis using STRING software permitted to build an interactomic map of all detected proteins, characterised by 34 interactions...
January 15, 2018: Food Chemistry
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