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Network protein function prediction

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https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#1
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28724614/nuclear-mtor-acts-as-a-transcriptional-integrator-of-the-androgen-signaling-pathway-in-prostate-cancer
#2
Étienne Audet-Walsh, Catherine R Dufour, Tracey Yee, Fatima Z Zouanat, Ming Yan, Georges Kalloghlian, Mathieu Vernier, Maxime Caron, Guillaume Bourque, Eleonora Scarlata, Lucie Hamel, Fadi Brimo, Armen G Aprikian, Jacques Lapointe, Simone Chevalier, Vincent Giguère
Androgen receptor (AR) signaling reprograms cellular metabolism to support prostate cancer (PCa) growth and survival. Another key regulator of cellular metabolism is mTOR, a kinase found in diverse protein complexes and cellular localizations, including the nucleus. However, whether nuclear mTOR plays a role in PCa progression and participates in direct transcriptional cross-talk with the AR is unknown. Here, via the intersection of gene expression, genomic, and metabolic studies, we reveal the existence of a nuclear mTOR-AR transcriptional axis integral to the metabolic rewiring of PCa cells...
July 19, 2017: Genes & Development
https://www.readbyqxmd.com/read/28713998/identification-of-micrornas-in-acute-respiratory-distress-syndrome-based-on-microrna-expression-profile-in-rats
#3
Yinghui Guan, Xiang Jin, Xingang Liu, Yuanping Huang, Man Wang, Xiaodan Li
Acute respiratory distress syndrome (ARDS) remains a severe disease associated with an ~40% mortality rate and as many as 200,000 new cases annually. MicroRNAs (miRNAs) have important roles in gene regulation and cancer development. The present study aimed to identify the potential roles of miRNAs in the pathogenesis and progression of ARDS. The miRNA expression profile of the GSE57223 dataset was downloaded from the Gene Expression Omnibus database. Following data normalization, differentially expressed miRNAs were identified using the t‑test method...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713977/analysis-of-gene-expression-profile-microarray-data-in-complex-regional-pain-syndrome
#4
Wulin Tan, Yiyan Song, Chengqiang Mo, Shuangjian Jiang, Zhongxing Wang
The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713939/microarray-analysis-reveals-key-genes-and-pathways-in-tetralogy-of-fallot
#5
Yue-E He, Hui-Xian Qiu, Jian-Bing Jiang, Rong-Zhou Wu, Ru-Lian Xiang, Yuan-Hai Zhang
The aim of the present study was to identify key genes that may be involved in the pathogenesis of Tetralogy of Fallot (TOF) using bioinformatics methods. The GSE26125 microarray dataset, which includes cardiovascular tissue samples derived from 16 children with TOF and five healthy age‑matched control infants, was downloaded from the Gene Expression Omnibus database. Differential expression analysis was performed between TOF and control samples to identify differentially expressed genes (DEGs) using Student's t‑test, and the R/limma package, with a log2 fold‑change of >2 and a false discovery rate of <0...
July 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28705884/quantitative-analysis-of-protein-interaction-network-dynamics-in-yeast
#6
Albi Celaj, Ulrich Schlecht, Justin D Smith, Weihong Xu, Sundari Suresh, Molly Miranda, Ana Maria Aparicio, Michael Proctor, Ronald W Davis, Frederick P Roth, Robert P St Onge
Many cellular functions are mediated by protein-protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment-dependent protein complex dynamics, we used a DNA-barcode-based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments...
July 13, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28694066/disease-gene-classification-with-metagraph-representations
#7
Sezin Ata Kircali, Yuan Fang, Min Wu, Xiao-Li Li, Xiaokui Xiao
Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to exploit biological properties of individual proteins. More specifically, we integrate keywords describing protein properties into the PPI network, and construct a novel PPI-Keywords (PPIK) network consisting of both proteins and keywords as two different types of nodes...
July 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28693620/development-of-an-in-silico-method-for-the-identification-of-subcomplexes-involved-in-the-biogenesis-of-multiprotein-complexes-in-saccharomyces-cerevisiae
#8
Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin, Marie-Hélène Mucchielli-Giorgi
BACKGROUND: Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell processes can be extracted. We have developed an in silico approach based on these information to model the biogenesis of multiprotein complexes in the yeast Saccharomyces cerevisiae. RESULTS: Firstly, we have built three protein interaction networks by collecting the protein-protein interactions, which involved the subunits of three complexes, from different databases...
July 11, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28693226/screening-of-potentially-crucial-genes-and-regulatory-factors-involved-in-epithelial-ovarian-cancer-using-microarray-analysis
#9
Can Shi, Zhenyu Zhang
The present study aimed to screen potential genes implicated in epithelial ovarian cancer (EOC) and to further understand the molecular pathogenesis of EOC. In order to do this, datasets GSE14407 (containing 12 human ovarian cancer epithelia samples and 12 normal epithelia samples) and GSE29220 (containing 11 salivary transcriptomes from ovarian cancer patients with serous papillary adenocarcinoma and 11 matched controls) were obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) within these datasets were screened using the Linear Models for Microarray Data package, and potential gene functions were predicted by functional and pathway enrichment analyses...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28691014/drug-target-protein-protein-interaction-networks-a-systematic-perspective
#10
Yanghe Feng, Qi Wang, Tengjiao Wang
The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of them are based on either strong biological hypotheses or the chemical and physical properties of those targets separately. In this paper, we investigated three main ways to understand the functional biomolecules based on the topological features of drug targets. There are no significant differences between targets and common proteins in the protein-protein interactions network, indicating the drug targets are neither hub proteins which are dominant nor the bridge proteins...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28688561/uncovering-the-pathogenesis-of-microtia-using-bioinformatics-approach
#11
Liu Lei, Liu Zhenzhong, Lin Lin, Pan Bo
OBJECTIVE: Bioinformatics is widely used in the field of cancer research, but in the research of pathogenesis of congenital malformations the situation is different. The aim of this study was to explore the underlying mechanism using bioinformatics approach. METHODS: The data were available from Mouse Genome Informatics and Pubmed. Protein-protein interaction (PPI) network of pathogenic genes was conducted using STRING. Gene ontology and pathway enrichment analyses were also performed to pathogenic genes...
August 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28684341/near-perfect-protein-multi-label-classification-with-deep-neural-networks
#12
Balázs Szalkai, Vince Grolmusz
Biological sequences can be considered as data items of high-, non-fixed dimensions, corresponding to the length of those sequences. The comparison and the classification of biological sequences in their relations to large databases are important areas of research today. Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successful applications in image- and sound processing and classification problems. ANNs have also been applied for predicting the family or function of a protein, knowing its residue sequence...
July 3, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28683139/genome-wide-survey-of-heat-shock-factors-and-heat-shock-protein-70s-and-their-regulatory-network-under-abiotic-stresses-in-brachypodium-distachyon
#13
Feng Wen, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinshen Liu, Peng Li, Xiaojian Zhou, Xinxin Ji, Xiaomin Yue
The heat shock protein 70s (Hsp70s) and heat shock factors (Hsfs) play key roles in protecting plant cells or tissues from various abiotic stresses. Brachypodium distachyon, recently developed an excellent model organism for functional genomics research, is related to the major cereal grain species. Although B. distachyon genome has been fully sequenced, the information of Hsf and Hsp70 genes and especially the regulatory network between Hsfs and Hsp70s remains incomplete. Here, a total of 24 BdHsfs and 29 BdHsp70s were identified in the genome by bioinformatics analysis and the regulatory network between Hsfs and Hsp70s were performed in this study...
2017: PloS One
https://www.readbyqxmd.com/read/28682884/microarray-expression-profile-of-circular-rnas-in-chronic-thromboembolic-pulmonary-hypertension
#14
Ran Miao, Ying Wang, Jun Wan, Dong Leng, Juanni Gong, Jifeng Li, Yan Liang, Zhenguo Zhai, Yuanhua Yang
BACKGROUND: Chronic thromboembolic pulmonary hypertension (CTEPH) is a rare but debilitating and life-threatening complication of acute pulmonary embolism. Circular RNAs (circRNAs), presenting as covalently closed continuous loops, are RNA molecules with covalently joined 3'- and 5'-ends formed by back-splicing events. circRNAs may be significant biological molecules to understand disease mechanisms and to identify biomarkers for disease diagnosis and therapy. The aim of this study was to investigate the potential roles of circRNAs in CTEPH...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28680478/a-new-genome-scale-metabolic-model-of-corynebacterium-glutamicum-and-its-application
#15
Yu Zhang, Jingyi Cai, Xiuling Shang, Bo Wang, Shuwen Liu, Xin Chai, Tianwei Tan, Yun Zhang, Tingyi Wen
BACKGROUND: Corynebacterium glutamicum is an important platform organism for industrial biotechnology to produce amino acids, organic acids, bioplastic monomers, and biofuels. The metabolic flexibility, broad substrate spectrum, and fermentative robustness of C. glutamicum make this organism an ideal cell factory to manufacture desired products. With increases in gene function, transport system, and metabolic profile information under certain conditions, developing a comprehensive genome-scale metabolic model (GEM) of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28678323/expression-and-prognostic-roles-of-magnesium-dependent-phosphatase-1-in-gastric-cancer
#16
Y Chen, J Lin, M Yang, C-W Xu, B-Z Chen, X-J Li, W-F Zhu, W-D Fu, H Yu, M-G Ying, G Chen
OBJECTIVE: Gastric cancer is a leading cause of cancer deaths and has a poor prognosis after diagnosis. Previous studies showed that Magnesium-Dependent Phosphatase-1 (MDP-1) might be a key component for glycosylation in human protein repair, and an alteration of its function has been involved in some aspects of cellular metabolic networks linked to either normal or pathological processe. In this study, we investigate the MDP-1 status in patients with gastric carcinoma, and determine the potential relationship between MDP-1 and clinical outcome...
June 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28659828/formal-modeling-of-mtor-associated-biological-regulatory-network-reveals-novel-therapeutic-strategy-for-the-treatment-of-cancer
#17
Zurah Bibi, Jamil Ahmad, Amnah Siddiqa, Rehan Z Paracha, Tariq Saeed, Amjad Ali, Hussnain Ahmed Janjua, Shakir Ullah, Emna Ben Abdallah, Olivier Roux
Cellular homeostasis is a continuous phenomenon that if compromised can lead to several disorders including cancer. There is a need to understand the dynamics of cellular proliferation to get deeper insights into the prevalence of cancer. Mechanistic Target of Rapamycin (mTOR) is implicated as the central regulator of the metabolic pathway involved in growth whereas its two distinct complexes mTORC1 and mTORC2 perform particular functions in cellular propagation. To date, mTORC1 is a well defined therapeutic target to inhibit uncontrolled cell division, while the role of mTORC2 is not well characterized...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28643166/structural-disorder-in-plant-proteins-where-plasticity-meets-sessility
#18
REVIEW
Alejandra A Covarrubias, Cesar L Cuevas-Velazquez, Paulette S Romero-Pérez, David F Rendón-Luna, Caspar C C Chater
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks...
June 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28642634/analysis-of-map-kinase-mpk4-mekk1-mkk-genes-of-carica-papaya-l-comparative-to-other-plant-homologues
#19
Muhammad Hanam Hamid, Lina Rozano, Wee Chien Yeong, Janna Ong Abdullah, Noor Baity Saidi
Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species...
2017: Bioinformation
https://www.readbyqxmd.com/read/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#20
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
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