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Gene ontology, clustering

Hang Dong, Shuangfeng Shi, Chong Zhang, Sihui Zhu, Mei Li, Jie Tan, Yue Yu, Liping Lin, Shirong Jia, Xujing Wang, Yuanhua Wu, Yuhui Liu
BACKGROUND: Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. RESULTS: Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified...
May 18, 2018: BMC Genomics
Cynthia Kankeu, Kylie Clarke, Delphi Van Haver, Kris Gevaert, Francis Impens, Anna Dittrich, H Llewelyn Roderick, Egle Passante, Heinrich J Huber
The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis...
May 17, 2018: Molecular omics
Minjung Kim, Youngseok Yu, Ji-Hoi Moon, InSong Koh, Jae-Hyung Lee
Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering...
2018: International Journal of Genomics
Surjeet Kumar Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages...
May 15, 2018: Scientific Reports
Yu-Chun Chang, Yan Ding, Lingsheng Dong, Lang-Jing Zhu, Roderick V Jensen, Li-Li Hsiao
Background: Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these "housekeeping genes" (HKGs) could separate one normal human tissue type from another. Current focus on identifying "specific disease markers" is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers...
2018: PeerJ
Na An, Sheng Fan, Yibin Wang, Lizhi Zhang, Cai Gao, Dong Zhang, Mingyu Han
Recently, the long non-coding RNAs (lncRNAs), which play important roles in various complex biological processes, have received more attention in plants. However, little information is available on lncRNAs in woody fruit trees and their potential regulatory roles remain poorly understood, especially in apple. Here, a total of 1726 high-confidence lncRNAs (hc-lncRNAs) were identified in different tissues including young fruits, shoot tips, stem phloem and root tips using high-throughput sequencing. These lncRNAs are distributed across all 17 apple chromosomes, and >85% come from intergenic regions...
May 4, 2018: Gene
Hildegard Janouschek, Claudia R Eickhoff, Thomas W Mühleisen, Simon B Eickhoff, Thomas Nickl-Jockschat
Imaging genetics has become a highly popular approach in the field of schizophrenia research. A frequently reported finding is that effects from common genetic variation are associated with a schizophrenia-related structural endophenotype. Genetic contributions to a structural endophenotype may be easier to delineate, when referring to biological rather than diagnostic criteria. We used coordinate-based meta-analyses, namely the anatomical likelihood estimation (ALE) algorithm on 30 schizophrenia-related imaging genetics studies, representing 44 single-nucleotide polymorphisms at 26 gene loci investigated in 4682 subjects...
May 5, 2018: Brain Structure & Function
Juarez H Ferreira, Sarah S Cury, Ivan J Vechetti-Júnior, Geysson J Fernandez, Leonardo N Moraes, Carlos A B Alves, Paula P Freire, Carlos E A Freitas, Maeli Dal-Pai-Silva, Robson F Carvalho
Low-level laser irradiation (LLLI) has been used as a non-invasive method to improve muscular regeneration capability. However, the molecular mechanisms by which LLLI exerts these effects remain largely unknown. Here, we described global gene expression profiling analysis in C2C12 myoblasts after LLLI that identified 514 differentially expressed genes (DEG). Gene ontology and pathway analysis of the DEG revealed transcripts among categories related to cell cycle, ribosome biogenesis, response to stress, cell migration, and cell proliferation...
May 2, 2018: Lasers in Medical Science
Sugata Roy, Sebastian Schmeier, Bogumil Kaczkowski, Erik Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R R Forrest, Reto Guler, Vladimir B Bajic, Frank Brombacher, Harukazu Suzuki
Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes...
April 30, 2018: Scientific Reports
Ting Long, Zeyou Guo, Lu Han, Xiaoyan Yuan, Lei Liu, Wei Jing, Weidong Tian, Xiao-Hui Zheng, Wei Tang, Jie Long
Osteogenesis is a complex and tightly regulated process. Circular RNAs (circRNAs) are covalently closed RNA molecules which are thought to play a significant role in bone metabolism. The purpose of this study was to investigate the expression and putative function of circRNAs during the osteogenic differentiation of mouse adipose-derived stromal cells (mADSCs). circRNA microarrays were used to determine differential circRNAs expression at different stages during osteogenesis of mADSCs. The most frequent differentially expressed circRNAs were selected by Venn analysis and clustered among the three induced groups...
April 26, 2018: Calcified Tissue International
Jinlong Jian, Wei Wei, Guowei Yin, Aubryanna Hettinghouse, Chuanju Liu, Yongxiang Shi
p204, a murine member of the interferon-inducible p200 protein family, and its human analogue, IFI16, have been shown to function as tumor suppressors in vitro, but the molecular events involved, in particular in vivo, remain unclear. Herein we induced the Lewis Lung carcinoma (LLC) murine model of human lung cancer in p204 null mice (KO) and their control littermates (WT). We compared the transcriptome in spleen from WT and p204 KO mice using a high-throughput RNA-sequencing array. A total 30.02 Gb of clean data were obtained, and overall Q30% was greater than 90...
April 24, 2018: Scientific Reports
K Kranthi Kumar, B Uma Devi, P Neeraja
In this study, cholesterol biotransformation gene-set of human steroidogenic acute regulatory protein-related lipid transfer (START) domains were evaluated from high-throughput gene screening approaches. It was shown that STARD1, STARD3 and STARD4 proteins are better effective transporters of cholesterol than STARD5 and STARD6 domains. Docking studies show a strong agreement with gene ontology enrichment data. According to both complementary strategies, it was found that only STARD1, STARD3 and STARD4 are potentially involved in cholesterol biotransformation in mitochondria through Ω1-loop of C-terminal α4-helical domain...
April 24, 2018: SAR and QSAR in Environmental Research
Yan Li, Youtan Liu, Jun Fan, Quan Zhou, Xiuling Song, Zhiyong Peng, Zaisheng Qin, Tao Tao
Propofol, a widely used intravenous anesthetic, was previously considered as a neuroprotective agent. Recently, however, accumulating evidence suggests that it may cause neurotoxicity, especially in the development of neural stem cells (NSCs). The potential mechanisms contributing to propofol-induced neurotoxicity during neurogenesis, such as those involving microRNAs (miRNAs), are still unknown. In this study, a total of 27 differentially expressed miRNAs were identified in our initial screen and 6 miRNAs were validated by qRT-PCR...
April 18, 2018: Gene
Shuqin Zhang
BACKGROUND: Breast cancer and ovarian cancer are hormone driven and are known to have some predisposition genes in common such as the two well known cancer genes BRCA1 and BRCA2. The objective of this study is to compare the coexpression network modules of both cancers, so as to infer the potential cancer-related modules. METHODS: We applied the eigen-decomposition to the matrix that integrates the gene coexpression networks of both breast cancer and ovarian cancer...
April 11, 2018: BMC Systems Biology
Leilei Xia, Xiaoling Su, Jizi Shen, Qi Meng, Jiuqiong Yan, Caihong Zhang, Yu Chen, Han Wang, Mingjuan Xu
Background: Cervical cancer, one of the leading causes of female deaths, remains a top cause of mortality in gynecologic oncology and tends to affect younger individuals. However, the pathogenesis of cervical cancer is still far from clear. Given the high incidence and mortality of cervical cancer, uncovering the causes and pathogenesis as well as identifying novel biomarkers are of great significance and are desperately needed. Materials and methods: First, raw data were downloaded from the Gene Expression Omnibus database...
2018: Cancer Management and Research
Cyndia Mara Bezerra Dos Santos, Adriana Ludwig, Rafael Luis Kessler, Rita de Cássia Pontello Rampazzo, Alexandre Haruo Inoue, Marco Aurélio Krieger, Daniela Parada Pavoni, Christian Macagnan Probst
BACKGROUND Trypanosoma cruzi is an important protozoan parasite and the causative agent of Chagas disease. A critical step in understanding T. cruzi biology is the study of cellular and molecular features exhibited during its growth curve. OBJECTIVES We aimed to acquire a global view of the gene expression profile of T. cruzi during epimastigote growth. METHODS RNA-Seq analysis of total and polysomal/granular RNA fractions was performed along the 10 days T. cruzi epimastigote growth curve in vitro, in addition to cell viability and cell cycle analyses...
2018: Memórias do Instituto Oswaldo Cruz
Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, Maria L Gullino, Marc W Allard, Elena Levin, Davide Spadaro, Samir Droby
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M...
2018: Frontiers in Microbiology
Long-Ci Sun, Hai-Xin Qian
To identify biologically relevant genes associated with the pathogenesis of colorectal cancer (CRC), genome wide expression profiles of 17 pairs of CRC tumor and adjacent tissues, previously published in a DNA microarray study, were analyzed. Cytoscape, String tools and DAVID tools were used to investigate the biological pathways encoded by the genes identified as being either upregulated or downregulated in CRC, to determine protein‑protein interactions and to identify potential hub genes associated with CRC...
April 11, 2018: Molecular Medicine Reports
Shruti Choudhary, Sapna Thakur, Raoof Ahmad Najar, Aasim Majeed, Amandeep Singh, Pankaj Bhardwaj
Rhododendron arboreum, an ecologically prominent species, also lends commercial and medicinal benefits in the form of palatable juices and useful herbal-drugs. The local abundance and survival of the species under highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered the additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera...
April 15, 2018: Genome Génome / Conseil National de Recherches Canada
Jungnam Lee, Ivan Arisi, Ermanno Puxeddu, Lazarus K Mramba, Massimo Amicosante, Carmen M Swaisgood, Marco Pallante, Mark L Brantly, C Magnus Sköld, Cesare Saltini
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown cause characterized by alveolar epithelial damage, patchy interstitial fibrosis and diffuse microvascular abnormalities. In IPF, alveolar clustering of iron-laden alveolar macrophages-a common sign of microhemorrhage, has been associated with vascular abnormalities and worsening of pulmonary hypertension. As iron-dependent ROS generation has been shown to induce unrestrained macrophage activation in disease models of vascular damage, we explored alveolar macrophage activation phenotype in IPF patients (n = 16) and healthy controls (CTR, n = 7) by RNA sequencing of bronchoalveolar lavage (BAL) cells...
2018: PloS One
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