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Gene ontology, clustering

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https://www.readbyqxmd.com/read/29138116/in-silico-identification-of-genes-involved-in-chronic-metabolic-acidosis
#1
Ishfaq A Sheikh, Adeel Malik, Sameera F M AlBasri, Mohd A Beg
AIMS: Chronic metabolic acidosis (CMA) refers to increased plasma acidity due to disturbed acid-base equilibrium in human body. CMA leads to many dysfunctions including disorders of intestinal metabolism and barrier functions. The human body responds to these intestinal dysfunctions by creating a compensatory mechanism at genomic level in intestinal epithelial cells. This study was to identify the molecular pathways involved in metabolic dysfunction and compensatory adaptations in intestinal epithelium during CMA...
November 11, 2017: Life Sciences
https://www.readbyqxmd.com/read/29133276/de-novo-assembly-and-annotation-of-the-whole-genomic-analysis-of-vibrio-campbellii-rt-1-strain-from-infected-shrimp-litopenaeus-vannamei
#2
R Thirugnanasambandam, D Inbakandan, L Stanley Abraham, C Kumar, S M Sundaram, B Subashni, R Vasantharaja, A Arul Anantha Kumar, R Kirubagaran, S Ajmal Khan, T Balasubramanian
OBJECTIVES: This study aimed to sequence the whole genome of Vibrio campbellii RT-1 strain. METHODS: V. campbellii strain was isolated from an infected shrimp, Litopenaeus vannamei collected from aquaculture ponds, India (12.1899° N, 79.9249° E). The whole genome sequencing (WGS) was performed using the Illumina Hiseq 2500 platform and assembled de novo using SPAdes and Velvet optimiser. Furthermore, the gene prediction and annotation were performed by a rapid prokaryotic genome tool-Prokka...
November 10, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29131830/transcriptome-profiling-and-digital-gene-expression-analysis-of-sweet-potato-for-the-identification-of-putative-genes-involved-in-the-defense-response-against-fusarium-oxysporum-f-sp-batatas
#3
Yuli Lin, Weikun Zou, Shiqiang Lin, Dennis Onofua, Zhijian Yang, Haizhou Chen, Songliang Wang, Xuanyang Chen
Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61...
2017: PloS One
https://www.readbyqxmd.com/read/29126087/label-free-based-quantitative-proteomic-analysis-identifies-proteins-involved-in-the-testis-maturation-of-bactrocera-dorsalis-hendel
#4
Dong Wei, Meng-Yi Zhang, Pei-Ming Gu, Guy Smagghe, Jin-Jun Wang
Complex structural and biochemical processes take place in insect testis maturation, but the mechanisms by which functional proteins induce and regulate male fertility are unknown. Proteomics has been widely used to identify functional proteins involved in such complex physiological processes. In this study, we performed a label-free based quantitative proteomic analysis of developing testis of Bactrocera dorsalis with the aim of shedding light on spermatogenesis, sperm formation and also tissue development...
October 18, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29123635/er-yag-laser-and-cyclosporin-a-effect-on-cell-cycle-regulation-of-human-gingival-fibroblast-cells
#5
Hojjat-Allah Abbaszadeh, Ali Asghar Peyvandi, Yousef Sadeghi, Akram Safaei, Mona Zamanian-Azodi, Maryam Sadat Khoramgah, Mostafa Rezaei-Tavirani
Introduction: Periodontitis is a set of inflammatory disorders characterized by periodontal attachment loss and alveolar bone resorption. Because of deficiency in periodontitis mechanical therapy, this study was aimed to explore the molecular influence of the erbiumdoped: yttrium aluminum garnet (Er:YAG) laser and cyclosporin A (CsA) on human gingival fibroblasts (HGFs) for improvement in periodontal diseases therapy. Methods: We focused on articles that studied the proteome profiles of HGFs after treatment with laser irradiation and application of CsA...
2017: Journal of Lasers in Medical Sciences
https://www.readbyqxmd.com/read/29123525/identification-of-new-features-from-known-bacterial-protective-vaccine-antigens-enhances-rational-vaccine-design
#6
Edison Ong, Mei U Wong, Yongqun He
With many protective vaccine antigens reported in the literature and verified experimentally, how to use the knowledge mined from these antigens to support rational vaccine design and study underlying design mechanism remains unclear. In order to address the problem, a systematic bioinformatics analysis was performed on 291 Gram-positive and Gram-negative bacterial protective antigens with experimental evidence manually curated in the Protegen database. The bioinformatics analyses evaluated included subcellular localization, adhesin probability, peptide signaling, transmembrane α-helix and β-barrel, conserved domain, Clusters of Orthologous Groups, and Gene Ontology functional annotations...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29119738/physiological-characterization-transcriptomic-profiling-and-microsatellite-marker-mining-of-lycium-ruthenicum
#7
Jin-Huan Chen, Dong-Zhi Zhang, Chong Zhang, Mei-Long Xu, Wei-Lun Yin
Lycium ruthenicum is a perennial shrub species that has attracted considerable interest in recent years owing to its nutritional value and ability to thrive in a harsh environment. However, only extremely limited transcriptomic and genomic data related to this species can be found in public databases, thereby limiting breeding research and molecular function analysis. In this study, we characterized the physiological and biochemical responses to saline-alkaline mixed stress by measuring photochemical efficiency, chlorophyll content, and protective enzyme activity...
2017: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/29116075/-differential-alternative-splicing-in-brain-regions-of-rats-selected-for-aggressive-behavior
#8
V N Babenko, A O Bragin, I V Chadaeva, A L Markel, Y L Orlov
Profiles of alternative mRNA isoforms have been determined in three brain regions of rats from an aggressive and a tame line selected for 74 generations. Among 2319 genes with alternatively spliced exons, approximately 84% were confirmed by analyzing public databases. Based on Gene Ontology-guided clustering of alternatively spliced genes, it has been found that the sample was enriched in synapse-specific genes (FDR < 10^(-17)). Patterns of gene expression in the brains of animals with genetically determined high or low aggression were more frequently found to differ in the use of alternatively spliced exons than in animals environmentally conditioned for increased or lowered propensity to aggression...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29115427/abnormal-dna-methylation-may-contribute-to-the-progression-of-osteosarcoma
#9
Xiao-Gang Chen, Liang Ma, Jia-Xin Xu
The identification of optimal methylation biomarkers to achieve maximum diagnostic ability remains a challenge. The present study aimed to elucidate the potential molecular mechanisms underlying osteosarcoma (OS) using DNA methylation analysis. Based on the GSE36002 dataset obtained from the Gene Expression Omnibus database, differentially methylated genes were extracted between patients with OS and controls using t‑tests. Subsequently, hierarchical clustering was performed to segregate the samples into two distinct clusters, OS and normal...
October 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29115421/gene-expression-profiles-and-protein%C3%A2-protein-interaction-networks-during-tongue-carcinogenesis-in-the-tumor-microenvironment
#10
Wei Sun, Zeting Qiu, Wenqi Huang, Minghui Cao
Oral tongue squamous cell carcinoma (OTSCC) has a high incidence and is associated with a high mortality rate. Studies regarding the potential molecular mechanism of OTSCC in the tumor microenvironment (TME) are required. The present study aimed to perform bioinformatic analysis to identify important nodes, clusters and functional pathways during tongue carcinogenesis in the TME. After downloading the gene expression data of GSE42780, differentially expressed genes (DEGs) among carcinoma, dysplastic and normal samples in epithelia and fibroblasts were identified using the affy and limma packages with R version 3...
October 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29115411/transcriptome-sequencing-revealed-candidate-genes-relevant-to-mesenchymal-stem-cells-role-in-aortic-dissection-patients
#11
Junlin Yang, Sili Zou, Mingfang Liao, Lefeng Qu
Aortic dissection (AD) results from the imbalance between synthesis and degradation of extracellular matrices in aortic wall, which is characterized by chronic inflammation. Mesenchymal stem cells (MSCs) are known for anti‑inflammatory and repairing effects and have therefore been studied for treatment for numerous diseases, including AD. However, it is unclear which genes or signaling pathways contribute to MSCs' role in AD. In the present study, RNA sequencing (RNA‑seq) was conducted between MSCs from patients with AS (AD‑MSCs) and those from age‑matched healthy donors (HD‑MSCs)...
October 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29115400/global-gene-expression-analysis-combined-with-a-genomics-approach-for-the-identification-of-signal-transduction-networks-involved-in-postnatal-mouse-myocardial-proliferation-and-development
#12
Ruoxin Wang, Chao Su, Xinting Wang, Qiang Fu, Xingjie Gao, Chunyan Zhang, Jie Yang, Xi Yang, Minxin Wei
Mammalian cardiomyocytes may permanently lose their ability to proliferate after birth. Therefore, studying the proliferation and growth arrest of cardiomyocytes during the postnatal period may enhance the current understanding regarding this molecular mechanism. The present study identified the differentially expressed genes in hearts obtained from 24 h‑old mice, which contain proliferative cardiomyocytes; 7‑day‑old mice, in which the cardiomyocytes are undergoing a proliferative burst; and 10‑week‑old mice, which contain growth‑arrested cardiomyocytes, using global gene expression analysis...
November 3, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29113811/incorporating-gene-ontology-into-fuzzy-relational-clustering-of-microarray-gene-expression-data
#13
Animesh Kumar Paul, Pintu Chandra Shill
The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of the cell. In this paper, we propose gene ontology (GO) annotations based semi-supervised clustering algorithm called GO fuzzy relational clustering (GO-FRC) where one gene is allowed to be assigned to multiple clusters which are the most biologically relevant behavior of genes...
November 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/29113181/microrna-profiling-and-bioinformatics-analyses-reveal-the-potential-roles-of-micrornas-in-chordoma
#14
Kangwu Chen, Hao Chen, Kai Zhang, Siwei Sun, Jianqiang Mo, Jian Lu, Zhonglai Qian, Huilin Yang
Chordoma is a rare aggressive bone tumor arising from remnants of the notochord, and patients with chordoma have a poor prognosis. However, the unique expression profiles of microRNAs (miRNAs/miRs) and their downstream signaling pathways in chordoma remain incompletely characterized. The aim of the present study was to delineate the global miRNA expression profile and associated signaling networks in chordoma. miRNA profiling was performed on chordoma and fetal notochord tissues. Differentially expressed miRNAs in chordoma were analyzed using microarrays with hierarchical clustering analysis...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29102647/the-transcriptional-landscape-of-radiation-treated-human-prostate-cancer-analysis-of-a-prospective-tissue-cohort
#15
Simon P Keam, Franco Caramia, Cristina Gamell, Piotr J Paul, Gisela Mir Arnau, Paul J Neeson, Scott G Williams, Ygal Haupt
PURPOSE: The resistance of prostate cancer to radiation therapy (RT) is a significant clinical issue and still largely unable to be guided by patient-specific molecular characteristics. The present study describes the gene expression changes induced in response to RT in human prostate tissue obtained from a prospective tissue acquisition study designed for radiobiology research. METHODS AND MATERIALS: A prospective cohort of 5 men with intermediate-risk and clinically localized tumors were treated with high-dose-rate brachytherapy with 2 × 10-Gy fractions...
September 25, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29082700/-anti-inflammatory-mechanism-analysis-of-antirheumatic-chinese-medicinal-herb-aconiti-radix-based-on-protein-interaction-network
#16
Shi-Chao Zheng, Xiao-Ying Yan, Ju Chen, Shu-Ting Zhao, Chuan-Biao Wen
Inflammation is one of the important risk factors of rheumatic diseases. Aconiti Radix is widely used for the treatment of rheumatism, which has significant anti-inflammatory effects. However, its anti-inflammatory mechanism on molecular level is still not clear. The purpose of this study is to illuminate the anti-inflammatory mechanism of Aconiti Radix based on the protein interaction network (PIN) analysis on molecular network level. The main anti-inflammatory components (aconitine, hypaconitine and mesaconitine) were chosen in this study to obtain the targets of the components and protein-protein information though databases retrieval and construct the PIN of Aconiti Radix...
May 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29079755/a-proteome-view-of-structural-functional-and-taxonomic-characteristics-of-major-protein-domain-clusters
#17
Chia-Tsen Sun, Austin W T Chiang, Ming-Jing Hwang
Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29069456/thyroid-state-regulates-gene-expression-in-human-whole-blood
#18
Elske T Massolt, Marcel E Meima, Sigrid M A Swagemakers, Selmar Leeuwenburgh, Mirjam C G M van den Hout-van Vroonhoven, Giulia Brigante, Boen L R Kam, Peter J van der Spek, Wilfred F J van IJcken, Theo J Visser, Robin P Peeters, W Edward Visser
Context: Despite the well-recognized clinical features due to insufficient or excessive thyroid hormone (TH) levels in humans, it is largely unknown which genes are regulated by TH in human tissues. Objective: To study the effect of TH on human gene expression profiles in whole blood, mainly consisting of TRα-expressing cells. Methods: We performed next-generation RNA sequencing on whole blood samples from 8 athyroid patients (4 females) on and after 4 weeks off levothyroxine replacement...
October 23, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29066302/de-novo-transcriptomic-analysis-during-lentinula-edodes-fruiting-body-growth
#19
Yingzhu Wang, Xianlu Zeng, Wenguang Liu
The fruiting body of Lentinula edodes is a popular edible mushroom, and extracts from the mycelium and the fruiting body of this species have diverse therapeutic potential. To gain insights into the molecular mechanisms underlying the fruiting body growth of L. edodes from the early bud stage (EBS), through the intermediate developing stage (IDS), to the fully developed stage (FDS), we performed de novo transcriptomic analysis using high-throughput Illumina RNA-sequencing. First, we generated three cDNA libraries representative of the three respective stages...
October 21, 2017: Gene
https://www.readbyqxmd.com/read/29059200/de-novo-rna-sequencing-transcriptome-of-rhododendron-obtusum-identified-the-early-heat-response-genes-involved-in-the-transcriptional-regulation-of-photosynthesis
#20
Linchuan Fang, Jun Tong, Yanfang Dong, Dongyun Xu, Jing Mao, Yuan Zhou
Rhododendron spp. is an important ornamental species that is widely cultivated for landscape worldwide. Heat stress is a major obstacle for its cultivation in south China. Previous studies on rhododendron principally focused on its physiological and biochemical processes, which are involved in a series of stress tolerance. However, molecular or genetic properties of rhododendron's response to heat stress are still poorly understood. The phenotype and chlorophyll fluorescence kinetics parameters of four rhododendron cultivars were compared under normal or heat stress conditions, and a cultivar with highest heat tolerance, "Yanzhimi" (R...
2017: PloS One
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