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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/28505379/analysis-of-cfb-a-cytokinin-responsive-gene-of-arabidopsis-thaliana-encoding-a-novel-f-box-protein-regulating-sterol-biosynthesis
#1
Wolfram G Brenner, Jan Erik Leuendorf, Anne Cortleven, Laetitia B B Martin, Hubert Schaller, Thomas Schmülling
Protein degradation by the ubiquitin-26S proteasome pathway is important for the regulation of cellular processes, but the function of most F-box proteins relevant to substrate recognition is unknown. We describe the analysis of the gene Cytokinin-induced F-box encoding (CFB, AT3G44326), identified in a meta-analysis of cytokinin-related transcriptome studies as one of the most robust cytokinin response genes. F-box domain-dependent interaction with the E3 ubiquitin ligase complex component ASK1 classifies CFB as a functional F-box protein...
May 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28500704/meta-analysis-of-the-transcriptome-reveals-a-core-set-of-shade-avoidance-genes-in-arabidopsis
#2
Romina Sellaro, Manuel Pacín, Jorge J Casal
The presence of neighboring vegetation modifies the light input perceived by photo-sensory receptors, initiating a signaling cascade that adjusts plant growth and physiology. Thousands of genes can change their expression during this process, but the structure of the transcriptional circuit is poorly understood. Here we present a meta-analysis of transcriptome data from Arabidopsis thaliana exposed to neighbor signals in different contexts, including organs where growth is promoted or inhibited by these signals...
May 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28494519/molecular-insights-into-cassava-brown-streak-virus-susceptibility-and-resistance-by-profiling-of-the-early-host-response
#3
Ravi B Anjanappa, Devang Mehta, Michal J Okoniewski, Alicja Szabelska, Wilhelm Gruissem, Hervé Vanderschuren
Cassava brown streak viruses (CBSVs) are responsible for significant cassava yield losses in eastern sub-Saharan Africa. To study the possible mechanisms of plant resistance to CBSVs we inoculated CBSV-susceptible and -resistant cassava varieties with a mixed infection of CBSVs using top-cleft grafting. Transcriptome profiling of the two cassava varieties was performed at the earliest time-point of full infection (28 days after grafting) in the susceptible scions. The expression of genes encoding proteins in RNA silencing, salicylic acid pathways and callose deposition was altered in the susceptible cassava variety but transcriptional changes were limited in the resistant variety...
May 11, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28474265/gene-expression-signatures-for-head-and-neck-cancer-patient-stratification-are-results-ready-for-clinical-application
#4
REVIEW
Luca Tonella, Marco Giannoccaro, Salvatore Alfieri, Silvana Canevari, Loris De Cecco
Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer by incidence worldwide and considering the recent EUROCARE-5 population-based study the 5-year survival rate of HNSCC patients in Europe ranges between 69% in localized cases and 34% in patients with regional involvement. The development of high-throughput gene expression assays in the last two decades has provided the invaluable opportunity to improve our knowledge on cancer biology and to identify predictive signatures in the most deeply analyzed malignancies, such as hematological and breast cancers...
May 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/28460316/a-comprehensive-regional-analysis-of-genome-wide-expression-profiles-for-major-depressive-disorder
#5
Diego A Forero, Gina P Guio-Vega, Yeimy González-Giraldo
BACKGROUND: Major depressive disorder (MDD) is a global health challenge. In recent years, a large number of genome-wide expression studies (GWES) have been carried out to identify the transcriptomic profiles for MDD. The objective of this work was to carry out a comprehensive meta-analysis of available GWES for MDD. METHODS: GWES for MDD with available raw data were searched in NCBI GEO, Array Express and Stanley databases. Raw GWES data were preprocessed and normalized and meta-analytical procedures were carried out with the Network Analyst program...
April 26, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#6
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28424608/blood-transcriptomic-meta-analysis-identifies-dysregulation-of-hemoglobin-and-iron-metabolism-in-parkinson-disease
#7
Jose A Santiago, Judith A Potashkin
Disrupted iron metabolism has been implicated in the pathogenesis of Parkinson's disease (PD), a progressive neurodegenerative disorder that severely affects movement and coordination, yet the molecular mechanisms underlying this association remain unknown. To this end, we performed a transcriptomic meta-analysis of four blood microarrays in PD. We observed a significant downregulation of genes related to hemoglobin including, hemoglobin delta (HBD), alpha hemoglobin stabilizing protein (ASHP), genes implicated in iron metabolism including, solute carrier family 11 member 2 (SLC11A2), ferrochelatase (FECH), and erythrocyte-specific genes including erythrocyte membrane protein (EPB42), and 5'-aminolevulinate synthase 2 (ALAS2)...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28418402/transcriptome-sequencing-study-implicates-immune-related-genes-differentially-expressed-in-schizophrenia-new-data-and-a-meta-analysis
#8
A R Sanders, E I Drigalenko, J Duan, W Moy, J Freda, H H H Göring, P V Gejman
We undertook an RNA sequencing (RNAseq)-based transcriptomic profiling study on lymphoblastoid cell lines of a European ancestry sample of 529 schizophrenia cases and 660 controls, and found 1058 genes to be differentially expressed by affection status. These differentially expressed genes were enriched for involvement in immunity, especially the 697 genes with higher expression in cases. Comparing the current RNAseq transcriptomic profiling to our previous findings in an array-based study of 268 schizophrenia cases and 446 controls showed a highly significant positive correlation over all genes...
April 18, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28401644/comprehensive-dissection-of-transcriptome-data-and-regulatory-factors-in-pancreatic-cancer-cells
#9
Bijan Akbari, Abdulshakour Mohammadnia, Moein Yaqubi, Ping Wee, Hamid Mahdiuni
Features of pancreatic cancers include high mortality rates caused by rapid tumor progression and a lack of effective therapy. Underpinning the molecular mechanisms involved in the alteration of the gene expression program in the pancreatic cancer remains to be understood. In the current study we performed a comprehensive analysis using 282 pancreatic tumor and normal samples from seven independent expression data sets to provide a better view on the interactions between different transcription factors (TFs) and the most affected biological pathways in pancreatic cancer...
April 12, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28390038/integrative-transcriptome-analysis-of-liver-cancer-profiles-identifies-upstream-regulators-and-clinical-significance-of-acsm3-gene-expression
#10
Ramani Gopal, Karthikeyan Selvarasu, Ponmathi Panneer Pandian, Kumaresan Ganesan
PURPOSE: Hepatocellular carcinoma (HCC) is one of the most common human malignancies. It has frequently been associated with metabolic perturbations and liver damages. Various members of the family of acyl-CoA synthetases are known to be involved in the production of bioactive fatty acids, and altered expression of its encoding genes has been found to be involved in metabolic perturbations. For the development of novel diagnostic and therapeutic HCC options, a fundamental understanding of the mechanisms associated with the deregulation of candidate genes involved in metabolic perturbation is required...
April 7, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28363426/molecular-pathology-of-skeletal-growth-anomalies-in-the-brain-coral-platygyra-carnosa-a-meta-transcriptomic-analysis
#11
Yu Zhang, Jin Sun, Huawei Mu, Janice C Y Lun, Jian-Wen Qiu
Coral skeletal growth anomaly (GA) is a common coral disease. Although extensive ecological characterizations of coral GA have been performed, the molecular pathology of this disease remains largely unknown. We compared the meta-transcriptome of normal and GA-affected polyps of Platygyra carnosa using RNA-Seq. Approximately 50 million sequences were generated from four pairs of normal and GA-affected tissue samples. There were 109 differentially expressed genes (DEGs) in P. carnosa and 31 DEGs in the coral symbiont Symbiodinium sp...
March 28, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28362817/cis-eqtl-based-trans-ethnic-meta-analysis-reveals-novel-genes-associated-with-breast-cancer-risk
#12
Joshua D Hoffman, Rebecca E Graff, Nima C Emami, Caroline G Tai, Michael N Passarelli, Donglei Hu, Scott Huntsman, Dexter Hadley, Lancelote Leong, Arunabha Majumdar, Noah Zaitlen, Elad Ziv, John S Witte
Breast cancer is the most common solid organ malignancy and the most frequent cause of cancer death among women worldwide. Previous research has yielded insights into its genetic etiology, but there remains a gap in the understanding of genetic factors that contribute to risk, and particularly in the biological mechanisms by which genetic variation modulates risk. The National Cancer Institute's "Up for a Challenge" (U4C) competition provided an opportunity to further elucidate the genetic basis of the disease...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28357032/meta-analysis-reveals-up-regulation-of-cholesterol-processes-in-non-alcoholic-and-down-regulation-in-alcoholic-fatty-liver-disease
#13
Wasco Wruck, James Adjaye
AIM: To compare transcriptomes of non-alcoholic fatty liver disease (NAFLD) and alcoholic liver disease (ALD) in a meta-analysis of liver biopsies. METHODS: Employing transcriptome data from patient liver biopsies retrieved from several public repositories we performed a meta-analysis comparing ALD and NAFLD. RESULTS: We observed predominating commonalities at the transcriptome level between ALD and NAFLD, most prominently numerous down-regulated metabolic pathways and cytochrome-related pathways and a few up-regulated pathways which include ECM-receptor interaction, phagosome and lysosome...
March 18, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28335819/concordance-analysis-of-microarray-studies-identifies-representative-gene-expression-changes-in-parkinson-s-disease-a-comparison-of-33-human-and-animal-studies
#14
COMPARATIVE STUDY
Erin Oerton, Andreas Bender
BACKGROUND: As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. METHODS: In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease...
March 23, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#15
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334340/meta-analytic-framework-for-liquid-association
#16
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28329862/the-transcriptome-of-the-zebrafish-embryo-after-chemical-exposure-a-meta-analysis
#17
Andreas Schüttler, Kristin Reiche, Rolf Altenburger, Wibke Busch
Numerous studies have been published in the past years investigating the transcriptome of the zebrafish embryo (ZFE) upon being subjected to chemical stress. Aiming at a more mechanistic understanding of the results of such studies, knowledge about commonalities of transcript regulation in response to chemical stress is needed. Thus, our goal in this study was to identify and interpret genes and gene sets constituting a general response to chemical exposure. Therefore, we aggregated and reanalyzed published toxicogenomics data obtained with the ZFE...
February 27, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28320322/exploring-the-nature-of-prediagnostic-blood-transcriptome-markers-of-chronic-lymphocytic-leukemia-by-assessing-their-overlap-with-the-transcriptome-at-the-clinical-stage
#18
Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A Kyrtopoulos, Ingvar A Bergdahl, Ann-Sofie Johansson, Dennie D G A J Hebels, Theo M C M de Kok, Paolo Vineis, Roel C H Vermeulen
BACKGROUND: We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched controls. We hypothesized that a large fraction of these markers were likely related to early disease manifestations. Here we aim to gain a better understanding of the natural history of the identified markers by comparing results from our prediagnostic analysis, the only prediagnostic analysis to date, to results obtained from a meta-analysis of a series of publically available transcriptomics profiles obtained in incident CLL cases and controls...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28295046/transcriptomic-immaturity-of-the-hippocampus-and-prefrontal-cortex-in-patients-with-alcoholism
#19
Tomoyuki Murano, Hisatsugu Koshimizu, Hideo Hagihara, Tsuyoshi Miyakawa
Alcoholism, which is defined as the recurring harmful use of alcohol despite its negative consequences, has a lifetime prevalence of 17.8%. Previous studies have shown that chronic alcohol consumption disrupts various brain functions and behaviours. However, the precise mechanisms that underlie alcoholism are currently unclear. Recently, we discovered "pseudo-immature" brain cell states of the dentate gyrus and prefrontal cortex (PFC) in mouse models of psychotic disorders and epileptic seizure. Similar pseudo-immaturity has been observed in patients with psychotic disorders, such as schizophrenia and bipolar disorder...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28250240/atrx-a-novel-progesterone-regulated-biomarker-of-mammalian-oocyte-developmental-potential
#20
Lynne Clare O'Shea, Edward Daly, Carmel Hensey, Trudee Fair
A multi-species meta-analysis of published transcriptomic data from models of oocyte competence identified the chromatin remodelling factor ATRX, as a putative biomarker of oocyte competence. The objective of the current study was to test the hypothesis that ATRX protein expression by cumulus oocyte complexes (COCs) reflects their intrinsic quality and developmental potential. In excess of 10,000 bovine COCs were utilized to test our hypothesis. COCs were in vitro matured (IVM) under conditions associated with reduced developmental potential: IVM in the presence or absence of (1) progesterone synthesis inhibitor (Trilostane); (2) nuclear progesterone receptor inhibitor (Aglepristone) or (3) an inducer of DNA damage (Staurosporine)...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
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