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Gene ontology, clustering

Julia Engelhorn, Franziska Turck
Genome-wide analyses of chromatin factor-binding sites or histone modification localization generate lists of up to several thousand potential target genes. For many model organisms, large annotation databases are available to help with the characterization and classification of genomic datasets. The term meta-analysis has been coined for this type of multi-database comparison. In this chapter, we describe a workflow to perform a transcriptional and functional analysis of genome-wide target genes. Sources of transcription data and clustering tools to subdivide genes according to their expression pattern are described...
2017: Methods in Molecular Biology
Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Yujie Jia, Kun Nie, Jing Li, Xinyue Liang, Xuezhu Zhang
In order to investigate the pathogenic targets and associated biological process of Alzheimer's disease in the present study, mRNA expression profiles (GSE28146) and microRNA (miRNA) expression profiles (GSE16759) were downloaded from the Gene Expression Omnibus database. In GSE28146, eight control samples, and Alzheimer's disease samples comprising seven incipient, eight moderate, seven severe Alzheimer's disease samples, were included. The Affy package in R was used for background correction and normalization of the raw microarray data...
October 12, 2016: Molecular Medicine Reports
Ru Zheng, Yue Li, Huiying Sun, Xiaoyin Lu, Bao-Fa Sun, Rui Wang, Lina Cui, Cheng Zhu, Hai-Yan Lin, Hongmei Wang
The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethylsulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h was sequenced...
October 14, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
Hui Zhang, Chuanchao Zhang, Jinting Yan, Zhongshuai Sun, Shuhui Song, Yazhou Sun, Caixia Guo
Spermatogenesis is threatened by DNA alkylating agents, one major category of DNA damaging agents. Currently, little is known about the alterations in transcriptome profiling of the mouse spermatogenic cells in response to DNA alkylation at distinct stages of spermatogenesis. In this study, RNA sequencing (RNA-seq) was performed in pachytene spermatocytes (PS) and round spermatids (RS) at 0 or 30min following Methyl Methanesulfonate (MMS) treatment and with untreated controls. A large number of differentially expressed genes (DEGs) were identified by comparison of the three groups in PS and RS, respectively...
October 5, 2016: Gene
Xinhe Huang, Yuxing Li, Jingmei Pan, Ming Li, Yongqin Lai, Jie Gao, Xueru Li
The nonessential metal cadmium can cause cell toxicity and is associated with a range of human diseases including cardiovascular diseases, neurodegenerative diseases and cancers. In this study, cadmium-induced global gene expression profile of yeast was obtained using RNA Sequencing (RNA-Seq) and further analyzed by means of informatics and experiments. A total of 912 Differentially Expressed Genes (DEGs) (FDR of q<0.01), including 415 Cd-inducible and 497 Cd-repressed genes were identified. Based on the DEGs, 25 cadmium responsive Clusters of Orthologous Group (COG) and three types of cadmium-induced Gene Ontology (GO) including cellular components, molecular functions and biological processes were analyzed in details...
October 7, 2016: Environmental Microbiology Reports
Tiantao Zhang, Kanglai He, Zhenying Wang
The Asian corn borer, Ostrinia furnacalis, is one of the most destructive pests of maize and causes huge losses in maize yield each year. In order to characterize the different developmental stages, a high-throughput sequencing platform was employed to perform de novo transcriptome assembly and gene expression analysis for the egg, larva, pupa and adult stages. Approximately 185 million reads were obtained, trimmed, and assembled into 42,638 unigenes with an average length of 801.94 bp and an N50 length of 1,152 bp...
October 7, 2016: Scientific Reports
Rucha Harishbhai Mehta, Manivel Ponnuchamy, Jitendra Kumar, Nagaraja Reddy Rama Reddy
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress...
October 5, 2016: Functional & Integrative Genomics
H Zhou, B H Cai, Z Q Lü, Z H Gao, Y S Qiao
Simple sequence repeats (SSRs), one of the most powerful molecular markers, can be used for DNA fingerprinting, variety identification, genetic mapping, and marker-assisted selection. Using the pear's (Pyrus pyrifolia Nakai) 75,764 unigenes (55,676,271 bp) obtained by deep transcriptome sequencing, a total of 10,622 novel SSRs were identified in 9154 unigenes, accounting for 14.02% of all unigenes. The average length and distribution of these SSRs was about 16 bp and 5.24 kb, respectively. Dinucleotide repeat motifs were the main type, with a frequency of 55...
September 23, 2016: Genetics and Molecular Research: GMR
Jun Liu, Ping Hua, Li Hui, Li-Li Zhang, Zhen Hu, Ying-Wei Zhu
The objective of this study was to identify hub genes and pathways associated with hepatocellular carcinoma (HCC) by centrality analysis of a co-expression network. A co-expression network based on differentially expressed (DE) genes of HCC was constructed using the Differentially Co-expressed Genes and Links (DCGL) package. Centrality analyses, for centrality of degree, clustering coefficient, closeness, stress and betweenness for the co-expression network were performed to identify hub genes, and the hub genes were combined together to overcome inconsistent results...
October 2016: Experimental and Therapeutic Medicine
Michele C R de Freitas, Juliana A Resende, Alessandra B Ferreira-Machado, Guadalupe D R Q Saji, Ana T R de Vasconcelos, Vânia L da Silva, Marisa F Nicolás, Cláudio G Diniz
Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug...
2016: Frontiers in Microbiology
Qian-Feng Li, Min Xiong, Peng Xu, Li-Chun Huang, Chang-Quan Zhang, Qiao-Quan Liu
Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice...
October 5, 2016: Scientific Reports
M Phan, F Conte, K D Khandelwal, C W Ockeloen, T Bartzela, T Kleefstra, H van Bokhoven, M Rubini, H Zhou, C E L Carels
Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia...
December 2016: Human Genetics
Jörn Lötsch, Alfred Ultsch
OBJECTIVE: The public accessibility of "big data" about the molecular targets of drugs and the biological functions of genes allows novel data science-based approaches to pharmacology that link drugs directly with their effects on pathophysiologic processes. This provides a phenotypic path to drug discovery and repurposing. This paper compares the performance of a functional genomics-based criterion to the traditional drug target-based classification. METHODS: Knowledge discovery in the DrugBank and Gene Ontology databases allowed the construction of a "drug target versus biological process" matrix as a combination of "drug versus genes" and "genes versus biological processes" matrices...
October 1, 2016: European Journal of Clinical Pharmacology
Cristina Camprubí, Albert Salas-Huetos, Riccardo Aiese-Cigliano, Anna Godo, Maria-Carme Pons, Giancarlo Castellano, Mark Grossmann, Walter Sanseverino, José I Martin-Subero, Nicolás Garrido, Joan Blanco
The influence of aberrant sperm DNA methylation on the reproductive capacity of couples has been postulated as a cause of infertility. This study compared the DNA methylation of spermatozoa of 19 fertile donors and 42 infertile patients using the Illumina 450K array. Clustering analysis of methylation data arranged fertile and infertile patients into two groups. Bivariate clustering analysis identified a differential distribution of samples according to the characteristics of seminogram and age, suggesting a possible link between these parameters and specific methylation profiles...
September 15, 2016: Reproductive Biomedicine Online
Chengli Zhang, Manchao Kuang, Meng Li, Lin Feng, Kaitai Zhang, Shujun Cheng
Structural maintenance of chromosome 4 (SMC4) is a core subunit of condensin complexes that mainly contributes to chromosome condensation and segregation. Our previous study demonstrated that the gene expression profile during lung development is of great values for the study of lung cancer. In this study, we identified SMC4 through co-expression network analysis and clique percolation clustering using genes that constant changes during four stages of lung development. Gene ontology and KEGG pathway enrichment analysis demonstrated that SMC4 is closely related to cell cycle, cell adhesion, and RNA processing in lung development and carcinogenesis...
September 30, 2016: Scientific Reports
Chen Chen, Jike Lu, Limin Hao, Zhiqiang Zheng, Naixun Zhang, Zhenyu Wang
To investigate the potential regulatory roles of microRNA (miRNA) in mouse response to ionizing radiation (IR)-induced thymus injury, miRNA expression profiles of mouse thymus with or without IR were analyzed using deep sequencing technology. Potential target candidates of the identified miRNA were predicted using RNAhybrid and miRanda. Differently expressed miRNA targets functional annotation and pathways were noted using Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and non-redundant (NR) databases...
August 11, 2016: International Journal of Radiation Biology
Carla Oseroff, Lars H Christensen, Luise Westernberg, John Pham, Jerome Lane, Sinu Paul, Jason Greenbaum, Thomas Stranzl, Gitte Lund, Ilka Hoof, Jens Holm, Peter A Würtzen, Kåre H Meno, April Frazier, Veronique Schulten, Peter S Andersen, Bjoern Peters, Alessandro Sette
BACKGROUND: House dust mite (HDM) allergens are a common cause of allergy and allergic asthma. A comprehensive analysis of proteins targeted by T cells, which are implicated in the development and regulation of allergic disease independent of their antibody reactivity, is still lacking. OBJECTIVE: To comprehensively analyze the HDM-derived protein targets of T cell responses in HDM-allergic individuals, and investigate their correlation with IgE/IgG responses and protein function...
September 29, 2016: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
Feng Liu, Jing-Bo Wu, Ru-Lin Zhan, Xiong-Chang Ou
Malformation caused by Fusarium mangiferae is one of the most destructive mango diseases affecting the canopy and floral development, leading to dramatic reduction in fruit yield. To further understand the mechanism of interaction between mango and F. mangiferae, we monitored the transcriptome profiles of buds from susceptible mango plants, which were challenged with F. mangiferae. More than 99 million reads were deduced by RNA-sequencing and were assembled into 121,267 unigenes. Based on the sequence similarity searches, 61,706 unigenes were identified, of which 21,273 and 50,410 were assigned to gene ontology categories and clusters of orthologous groups, respectively, and 33,243 were mapped to 119 KEGG pathways...
2016: Frontiers in Microbiology
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