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Gene annotation

Ya-Sian Chang, Chun-Chi Chang, Hsi-Yuan Huang, Chien-Yu Lin, Kun-Tu Yeh, Jan-Gowth Chang
Genetic and epigenetic alterations are associated with the progression and prognosis of medullary thyroid carcinoma (MTC). We performed whole-exome sequencing of tumor tissue from seven patients with sporadic MTC using an Illumina HiSeq 2000 sequencing system. We conducted Sanger sequencing to confirm the somatic mutations in both tumor and matched normal tissues. We applied Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis with the Database for Annotation, Visualization, and Integrated Discovery and STRING for pathway analysis...
August 17, 2018: Endocrine Pathology
Antonella Minutolo, Marina Potestà, Angelo Gismondi, Stefano Pirrò, Marco Cirilli, Fabiano Gattabria, Andrea Galgani, Libera Sessa, Maurizio Mattei, Antonella Canini, Rosario Muleo, Vittorio Colizzi, Carla Montesano
Functional foods include compounds with nutritional and health properties. The human diet could play a stronger role in cancer prevention. Only a few studies have described the presence of plant small RNA, in humans who were fed with plant foods, which demonstrated the ability of these molecules to modulate consumer's genes and evidenced the existence of a plant-animal regulation. Through in silico prediction, Olea europaea small RNAs (sRs), which had been previously reported as miRNAs, were identified, each with functional homology to hsa-miR34a...
August 17, 2018: Scientific Reports
Jinglan Jin, Hongqin Xu, Ruihong Wu, Junqi Niu, Shibo Li
PURPOSE: We aimed to study the aberrant DNA methylation profile associated with hepatitis B virus (HBV) infection and to identify key genes and pathways associated with the HBV infection stage. METHODS: A total of 54 antiviral treatment-naive HBV-infected patients and 6 healthy controls were included. Genome-wide methylated DNA immunoprecipitation analysis was performed, as previously described, after which the chip data were preprocessed. Subsequently, Cytoscape software was used for the construction of a protein-protein interaction network, and Database for Annotation, Visualization, and Integrated Discovery software was used to conduct functional enrichment analysis...
August 17, 2018: Journal of Medical Virology
Yongfu Xiong, Kang Wang, He Zhou, Linglong Peng, Wenxian You, Zhongxue Fu
Immune infiltration of colorectal cancer (CRC) is closely associated with clinical outcome. However, previous work has not accounted for the diversity of functionally distinct cell types that make up the immune response. In this study, based on a deconvolution algorithm (known as CIBERSORT) and clinical annotated expression profiles, we comprehensively analyzed the tumor-infiltrating immune cells present in CRC for the first time. The fraction of 22 immune cells subpopulations was evaluated to determine the associations between each cell type and survival and response to chemotherapy...
August 16, 2018: Cancer Medicine
Mónica Garcés-Ruiz, Carolina Senés-Guerrero, Stéphane Declerck, Sylvie Cranenbrouck
Arbuscular mycorrhizal fungi (AMF) are worldwide distributed plant symbionts. However, their occurrence in hydrocarbon-polluted environments is less investigated, although specific communities may be present with possible interest for remediation strategies. Here, we investigated the AMF community composition associated with the roots of diverse plant species naturally recolonizing a weathered crude oil pond in the Amazon region of Ecuador. Next generation 454 GS-Junior sequencing of an 800 bp LSU rRNA gene PCR amplicon was used...
August 16, 2018: MicrobiologyOpen
Linqian Han, Zhenna Mu, Zi Luo, Qingchun Pan, Lin Li
Long non-coding RNAs (lncRNAs), whose sequences are ∼200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize (Zea Mays L.) reference genome provides an essential genomic resource, genome-wide annotations of maize lncRNAs have not been updated (Jiao et al. 2017). Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte...
August 16, 2018: Journal of Integrative Plant Biology
Lin Wang, Shu Zhang, Jian-Hui Li, Yong-Jie Zhang
Nuclear genomes of two isolates of Hirsutella thompsonii, a pathogen causing epizootics among mites, have been reported; in contrast, its mitochondrial genome (mitogenome) has remained unknown, limiting our understanding of its evolution. Herein, we annotated the first complete mitogenome of H. thompsonii, which encoded all standard fungal mitochondrial genes plus three free-standing ORFs. Transcriptional analyses validated the expression of most conserved genes and revealed some interesting transcription patterns of mitochondrial genes...
August 16, 2018: Environmental Microbiology
Bo Jia, Zhaoqiang Zhang, Xiaoling Qiu, Hongxing Chu, Xiang Sun, Xianghuai Zheng, Jianjiang Zhao, Qin Li
Mesenchymal stem cells (MSCs) are bone marrow stromal cells capable of differentiating into different tissue types. Osteoblastic differentiation is a complex process that is critical for bone formation. An increasing number of studies have suggested that microRNAs (miRNAs) may serve important roles in various biological processes, including osteogenesis of MSCs. However, less is known about the participation of particular miRNAs in the osteogenic differentiation of adipose-derived stem cells (ADSCs). In order to identify functional miRNAs and the key genes involved in the osteogenesis of MSCs, the present study reconstructed a global network using data from the National Center for Biotechnology Information Gene Expression Omnibus...
August 2018: Experimental and Therapeutic Medicine
V Kalidasan, Adleen Azman, Narcisse Joseph, Suresh Kumar, Rukman Awang Hamat, Vasantha Kumari Neela
Iron has been shown to regulate biofilm formation, oxidative stress response and several pathogenic mechanisms in Stenotrophomonas maltophilia . Thus, the present study is aimed at identifying various iron acquisition systems and iron sources utilized during iron starvation in S. maltophilia . The annotations of the complete genome of strains K279a, R551-3, D457 and JV3 through Rapid Annotations using Subsystems Technology (RAST) revealed two putative subsystems to be involved in iron acquisition: the iron siderophore sensor and receptor system and the heme, hemin uptake and utilization systems/hemin transport system...
August 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Rudi Appels, Kellye Eversole, Catherine Feuillet, Beat Keller, Jane Rogers, Nils Stein, Curtis J Pozniak, Nils Stein, Frédéric Choulet, Assaf Distelfeld, Kellye Eversole, Jesse Poland, Jane Rogers, Gil Ronen, Andrew G Sharpe, Curtis Pozniak, Gil Ronen, Nils Stein, Omer Barad, Kobi Baruch, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Andrew G Sharpe, Gil Ben-Zvi, Ambre-Aurore Josselin, Nils Stein, Martin Mascher, Axel Himmelbach, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Jane Rogers, François Balfourier, Juan Gutierrez-Gonzalez, Matthew Hayden, Ambre-Aurore Josselin, ChuShin Koh, Gary Muehlbauer, Raj K Pasam, Etienne Paux, Curtis J Pozniak, Philippe Rigault, Andrew G Sharpe, Josquin Tibbits, Vijay Tiwari, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Ambre-Aurore Josselin, Jane Rogers, Manuel Spannagl, Frédéric Choulet, Daniel Lang, Heidrun Gundlach, Georg Haberer, Gabriel Keeble-Gagnère, Klaus F X Mayer, Danara Ormanbekova, Etienne Paux, Verena Prade, Hana Šimková, Thomas Wicker, Frédéric Choulet, Manuel Spannagl, David Swarbreck, Hélène Rimbert, Marius Felder, Nicolas Guilhot, Heidrun Gundlach, Georg Haberer, Gemy Kaithakottil, Jens Keilwagen, Daniel Lang, Philippe Leroy, Thomas Lux, Klaus F X Mayer, Sven Twardziok, Luca Venturini, Rudi Appels, Hélène Rimbert, Frédéric Choulet, Angéla Juhász, Gabriel Keeble-Gagnère, Frédéric Choulet, Manuel Spannagl, Daniel Lang, Michael Abrouk, Georg Haberer, Gabriel Keeble-Gagnère, Klaus F X Mayer, Thomas Wicker, Frédéric Choulet, Thomas Wicker, Heidrun Gundlach, Daniel Lang, Manuel Spannagl, Daniel Lang, Manuel Spannagl, Rudi Appels, Iris Fischer, Cristobal Uauy, Philippa Borrill, Ricardo H Ramirez-Gonzalez, Rudi Appels, Dominique Arnaud, Smahane Chalabi, Boulos Chalhoub, Frédéric Choulet, Aron Cory, Raju Datla, Mark W Davey, Matthew Hayden, John Jacobs, Daniel Lang, Stephen J Robinson, Manuel Spannagl, Burkhard Steuernagel, Josquin Tibbits, Vijay Tiwari, Fred van Ex, Brande B H Wulff, Curtis J Pozniak, Stephen J Robinson, Andrew G Sharpe, Aron Cory, Moussa Benhamed, Etienne Paux, Abdelhafid Bendahmane, Lorenzo Concia, David Latrasse, Jane Rogers, John Jacobs, Michael Alaux, Rudi Appels, Jan Bartoš, Arnaud Bellec, Hélène Berges, Jaroslav Doležel, Catherine Feuillet, Zeev Frenkel, Bikram Gill, Abraham Korol, Thomas Letellier, Odd-Arne Olsen, Hana Šimková, Kuldeep Singh, Miroslav Valárik, Edwin van der Vossen, Sonia Vautrin, Song Weining, Abraham Korol, Zeev Frenkel, Tzion Fahima, Vladimir Glikson, Dina Raats, Jane Rogers, Vijay Tiwari, Bikram Gill, Etienne Paux, Jesse Poland, Jaroslav Doležel, Jarmila Číhalíková, Hana Šimková, Helena Toegelová, Jan Vrána, Pierre Sourdille, Benoit Darrier, Rudi Appels, Manuel Spannagl, Daniel Lang, Iris Fischer, Danara Ormanbekova, Verena Prade, Delfina Barabaschi, Luigi Cattivelli, Pilar Hernandez, Sergio Galvez, Hikmet Budak, Burkhard Steuernagel, Jonathan D G Jones, Kamil Witek, Brande B H Wulff, Guotai Yu, Ian Small, Joanna Melonek, Ruonan Zhou, Angéla Juhász, Tatiana Belova, Rudi Appels, Odd-Arne Olsen, Kostya Kanyuka, Robert King, Kirby Nilsen, Sean Walkowiak, Curtis J Pozniak, Richard Cuthbert, Raju Datla, Ron Knox, Krysta Wiebe, Daoquan Xiang, Antje Rohde, Timothy Golds, Jaroslav Doležel, Jana Čížková, Josquin Tibbits, Hikmet Budak, Bala Ani Akpinar, Sezgi Biyiklioglu, Gary Muehlbauer, Jesse Poland, Liangliang Gao, Juan Gutierrez-Gonzalez, Amidou N'Daiye, Jaroslav Doležel, Hana Šimková, Jarmila Číhalíková, Marie Kubaláková, Jan Šafář, Jan Vrána, Hélène Berges, Arnaud Bellec, Sonia Vautrin, Michael Alaux, Françoise Alfama, Anne-Françoise Adam-Blondon, Raphael Flores, Claire Guerche, Thomas Letellier, Mikaël Loaec, Hadi Quesneville, Curtis J Pozniak, Andrew G Sharpe, Sean Walkowiak, Hikmet Budak, Janet Condie, Jennifer Ens, ChuShin Koh, Ron Maclachlan, Yifang Tan, Thomas Wicker, Frédéric Choulet, Etienne Paux, Adriana Alberti, Jean-Marc Aury, François Balfourier, Valérie Barbe, Arnaud Couloux, Corinne Cruaud, Karine Labadie, Sophie Mangenot, Patrick Wincker, Bikram Gill, Gaganpreet Kaur, Mingcheng Luo, Sunish Sehgal, Kuldeep Singh, Parveen Chhuneja, Om Prakash Gupta, Suruchi Jindal, Parampreet Kaur, Palvi Malik, Priti Sharma, Bharat Yadav, Nagendra K Singh, JitendraP Khurana, Chanderkant Chaudhary, Paramjit Khurana, Vinod Kumar, Ajay Mahato, Saloni Mathur, Amitha Sevanthi, Naveen Sharma, Ram Sewak Tomar, Jane Rogers, John Jacobs, Michael Alaux, Arnaud Bellec, Hélène Berges, Jaroslav Doležel, Catherine Feuillet, Zeev Frenkel, Bikram Gill, Abraham Korol, Edwin van der Vossen, Sonia Vautrin, Bikram Gill, Gaganpreet Kaur, Mingcheng Luo, Sunish Sehgal, Jan Bartoš, Kateřina Holušová, Ondřej Plíhal, Matthew D Clark, Darren Heavens, George Kettleborough, Jon Wright, Miroslav Valárik, Michael Abrouk, Barbora Balcárková, Kateřina Holušová, Yuqin Hu, Mingcheng Luo, Elena Salina, Nikolai Ravin, Konstantin Skryabin, Alexey Beletsky, Vitaly Kadnikov, Andrey Mardanov, Michail Nesterov, Andrey Rakitin, Ekaterina Sergeeva, Hirokazu Handa, Hiroyuki Kanamori, Satoshi Katagiri, Fuminori Kobayashi, Shuhei Nasuda, Tsuyoshi Tanaka, Jianzhong Wu, Rudi Appels, Matthew Hayden, Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Odd-Arne Olsen, Tatiana Belova, Federica Cattonaro, Min Jiumeng, Karl Kugler, Klaus F X Mayer, Matthias Pfeifer, Simen Sandve, Xu Xun, Bujie Zhan, Hana Šimková, Michael Abrouk, Jacqueline Batley, Philipp E Bayer, David Edwards, Satomi Hayashi, Helena Toegelová, Zuzana Tulpová, Paul Visendi, Song Weining, Licao Cui, Xianghong Du, Kewei Feng, Xiaojun Nie, Wei Tong, Le Wang, Philippa Borrill, Heidrun Gundlach, Sergio Galvez, Gemy Kaithakottil, Daniel Lang, Thomas Lux, Martin Mascher, Danara Ormanbekova, Verena Prade, Ricardo H Ramirez-Gonzalez, Manuel Spannagl, Nils Stein, Cristobal Uauy, Luca Venturini, Nils Stein, Rudi Appels, Kellye Eversole, Jane Rogers, Philippa Borrill, Luigi Cattivelli, Frédéric Choulet, Pilar Hernandez, Kostya Kanyuka, Daniel Lang, Martin Mascher, Kirby Nilsen, Etienne Paux, Curtis J Pozniak, Ricardo H Ramirez-Gonzalez, Hana Šimková, Ian Small, Manuel Spannagl, David Swarbreck, Cristobal Uauy
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development...
August 17, 2018: Science
Jianquan Zhao, Tiewei Lv, Junjun Quan, Weian Zhao, Jing Song, Zhuolin Li, Han Lei, Wei Huang, Longke Ran
BACKGROUND: Identify genes probably associated with chronic heart failure and predict potential target genes for dilated cardiomyopathy using bioinformatics analyses. METHODS: Gene expression profiles (series number GSE3585 and GSE42955) of cardiomyopathy patients and healthy controls were downloaded from the Expression Omnibus Gene (GEO) database. Differential expression of genes (DEGS) between the two groups of total 14 cardiomyopathy patients and 10 healthy controls were subsequently identified by limma package of R...
August 16, 2018: Journal of Biomedical Science
Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A Kuhlman, Stephan Q Schneider
BACKGROUND: The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. Its phylogenetic position within the spiralian/ lophotrochozoan clade, the comparatively high conservation of ancestral features in the Platynereis genome, and experimental access to any stage within its life cycle, make Platynereis an important model for elucidating the complex regulatory and functional molecular mechanisms governing early development, later organogenesis, and various features of its larval and adult life...
August 16, 2018: BMC Genomics
Xiujuan Lei, Xiaoqin Yang, Fangxiang Wu
It is well known that essential proteins play an extremely important role in controlling cellular activities in living organisms. Identifying essential proteins from protein protein interaction (PPI) networks is conducive to the understanding of cellular functions and molecular mechanisms. Hitherto, many essential proteins detection methods have been proposed. Nevertheless, those existing identification methods are not satisfactory because of low efficiency and low sensitivity to noisy data. This paper presents a novel computational approach based on artificial fish swarm optimization for essential proteins prediction in PPI networks (called AFSO_EP)...
August 15, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Alexandre Amlie-Wolf, Mitchell Tang, Elisabeth E Mlynarski, Pavel P Kuksa, Otto Valladares, Zivadin Katanic, Debby Tsuang, Christopher D Brown, Gerard D Schellenberg, Li-San Wang
The majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, affecting regulatory elements including transcriptional enhancers. However, characterizing their effects requires the integration of GWAS results with context-specific regulatory activity and linkage disequilibrium annotations to identify causal variants underlying noncoding association signals and the regulatory elements, tissue contexts, and target genes they affect. We propose INFERNO, a novel method which integrates hundreds of functional genomics datasets spanning enhancer activity, transcription factor binding sites, and expression quantitative trait loci with GWAS summary statistics...
August 3, 2018: Nucleic Acids Research
Wei Zhan, Celeste A Shelton, Phil J Greer, Randall E Brand, David C Whitcomb
Pancreatic cancer requires many genetic mutations. Combinations of underlying germline variants and environmental factors may increase the risk of cancer and accelerate the oncogenic process. We systematically reviewed, annotated, and classified previously reported pancreatic cancer-associated germline variants in established risk genes. Variants were scored using multiple criteria and binned by evidence for pathogenicity, then annotated with published functional studies and associated biological systems/pathways...
September 2018: Pancreas
R F Gubaev, V Y Gorshkov, L M Gapa, N E Gogoleva, E P Vetchinkina, Y V Gogolev
Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the genome sequence and its sufficient annotation for the target organism. However, a list of species with properly annotated genomes is limited. Transcriptome profiling is often performed in the so-called non-model organisms, which are those with unknown or poorly assembled and/or annotated genome sequences...
July 2018: Molekuliarnaia Biologiia
L-H Li, M-M Lv, X Li, T-Z Ye, X He, S-H Rong, Y-L Dong, Y Guan, X-L Gao, J-Q Zhu, Z-J Xu
With the advance of sequencing technology, the number of sequenced plant genomes has been rapidly increasing. However, understanding of the gene function in these sequenced genomes lags far behind; as a result, many coding plant sequences in public databases are annotated as proteins with domains of unknown function (DUF). Function of a protein family DUF810 in rice is not known. In this study, we analysed seven members of OsDU810 (OsDUF810.1-OsDUF810.7) family with three distinct motifs in rice Nipponbare...
July 2018: Molekuliarnaia Biologiia
Li-Juan Gao, Xin Zhao, Jian-Guo Li, Yong Xu, Yu Zhang
The aim of this study was to screen the genes related to the pathogenesis of major depression disorder (MDD) by bioinformatics. Taking GSE98793 chip data from GEO public database of National Biotechnology Information Center (NCBI) website as the research object, 116 differentially expressed genes (DEGs) were screened by R language limma package. Among the 116 DEGs, 66 genes were up-regulated and 50 down-regulated. The results of gene functional annotation analysis of Gene Ontology (GO) showed that the DEGs were mainly distributed in mitochondria intima and mitochondria...
August 25, 2018: Sheng Li Xue Bao: [Acta Physiologica Sinica]
Meng-Ting Gong, Shou-Dong Ye, Wen-Wen Lv, Kan He, Wen-Xing Li
Breast cancer is one of the primary threats to women's health worldwide. However, the molecular mechanisms underlying the development of breast cancer remain to be fully elucidated. The present study aimed to investigate specific target gene expression profiles in breast cancer tissues in general and in different breast cancer stages, as well as to explore their functions in tumor development. For integrated analysis, a total of 5 gene expression profiling datasets for 3 different stages of breast cancer (stages I-III) were downloaded from the Gene Expression Omnibus of the National Center for Biotechnology Information...
August 2018: Experimental and Therapeutic Medicine
Fozia Aslam, Azra Yasmin, Torsten Thomas
Stenotrophomonas MB339, a bacterium, which could potentially utilize aromatic compounds and tolerate different heavy metals was isolated from industrial wastewater. Subsequent experiments revealed strains ability to resist antibiotics ofloxacin, streptomycin, rifampicillin, erythromycin, ampicillin, clindamycin, and toxicants including As2+ , Hg2+ , Cu2+ , Ni2+ , Pb2+ . The shotgun sequencing strategy, genome assembly and annotation uncovered specific features, which make this strain MB339 effectively promising to cope with highly contaminated conditions...
August 14, 2018: Current Microbiology
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