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Gene ontology, clustering

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https://www.readbyqxmd.com/read/28197101/the-combination-of-three-components-derived-from-sheng-maisan-protects-myocardial-ischemic-diseases-and-inhibits-oxidative-stress-via-modulating-mapks-and-jak2-stat3-signaling-pathways-based-on-bioinformatics-approach
#1
Fang Li, Yu Zhang, Donglin Zeng, Yu Xia, Xiaoxue Fan, Yisha Tan, Junping Kou, Boyang Yu
GRS is a drug combination of three components including ginsenoside Rb1, ruscogenin and schisandrin. It derived from the well-known TCM formula Sheng MaiSan, a widely used traditional Chinese medicine for the treatment of cardiovascular diseases in clinic. The present study illuminates its underlying mechanisms against myocardial ischemic diseases based on the combined methods of bioinformatic prediction and experimental verification. A protein database was established through constructing the drug-protein network...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28196854/hypothalamic-transcriptomic-alterations-in-male-and-female-california-mice-peromyscus-californicus-developmentally-exposed-to-bisphenol-a-or-ethinyl-estradiol
#2
Sarah A Johnson, William G Spollen, Lindsey K Manshack, Nathan J Bivens, Scott A Givan, Cheryl S Rosenfeld
Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) prevalent in many household items. Rodent models and human epidemiological studies have linked this chemical to neurobehavior impairments. In California mice, developmental exposure to BPA results in sociosexual disorders at adulthood, including communication and biparental care deficits, behaviors that are primarily regulated by the hypothalamus. Thus, we sought to examine the transcriptomic profile in this brain region of juvenile male and female California mice offspring exposed from periconception through lactation to BPA or ethinyl estradiol (EE, estrogen present in birth control pills and considered a positive estrogen control for BPA studies)...
February 2017: Physiological Reports
https://www.readbyqxmd.com/read/28196101/de-novo-assembly-characterization-and-annotation-for-the-transcriptome-of-sarcocheilichthys-sinensis
#3
Chuankun Zhu, Zhengjun Pan, Hui Wang, Guoliang Chang, Nan Wu, Huaiyu Ding
The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved...
2017: PloS One
https://www.readbyqxmd.com/read/28187311/candidate-chemosensory-genes-identified-in-the-endoparasitoid-meteorus-pulchricornis-hymenoptera-braconidae-by-antennal-transcriptome-analysis
#4
Sheng Sheng, Cheng-Wu Liao, Yu Zheng, Yu Zhou, Yan Xu, Wen-Miao Song, Peng He, Jian Zhang, Fu-An Wu
Meteorus pulchricornis is an endoparasitoid wasp which attacks the larvae of various lepidopteran pests. We present the first antennal transcriptome dataset for M. pulchricornis. A total of 48,845,072 clean reads were obtained and 34,967 unigenes were assembled. Of these, 15,458 unigenes showed a significant similarity (E-value <10(-5)) to known proteins in the NCBI non-redundant protein database. Gene ontology (GO) and cluster of orthologous groups (COG) analyses were used to classify the functions of M...
January 31, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28183295/meta-analysis-of-gene-expression-in-relapsed-childhood-b-acute-lymphoblastic-leukemia
#5
Yock-Ping Chow, Hamidah Alias, Rahman Jamal
BACKGROUND: Relapsed pediatric B-acute lymphoblastic leukemia (B-ALL) remains as the leading cause of cancer death among children. Other than stem cell transplantation and intensified chemotherapy, no other improved treatment strategies have been approved clinically. Gene expression profiling represents a powerful approach to identify potential biomarkers and new therapeutic targets for various diseases including leukemias. However, inadequate sample size in many individual experiments has failed to provide adequate study power to yield translatable findings...
February 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28181037/de-novo-transcriptome-characterization-and-growth-related-gene-expression-profiling-of-diploid-and-triploid-bighead-catfish-clarias-macrocephalus-g%C3%A3-nther-1864
#6
Satid Chatchaiphan, Prapansak Srisapoome, Jin-Hyoung Kim, Robert H Devlin, Uthairat Na-Nakorn
To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases...
February 8, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28178938/messenger-rna-and-microrna-transcriptomic-signatures-of-cardiometabolic-risk-factors
#7
David D McManus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J Munson, Martin G Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane E Freedman, Daniel Levy
BACKGROUND: Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined associations of mRNA and miRNA levels with 6 CM traits: body mass index, HDL-cholesterol and triglycerides, fasting glucose, and systolic and diastolic blood pressures through cross-sectional analysis of 2812 Framingham Heart Study who had whole blood collection for RNA isolation for mRNA and miRNA expression studies and who consented to genetic research...
February 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28155727/an-improved-method-for-functional-similarity-analysis-of-genes-based-on-gene-ontology
#8
Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng
BACKGROUND: Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional similarity methods have been proposed based on the semantic similarity of GO terms. However, these leading approaches may make errorprone judgments especially when they measure the specificity of GO terms as well as the IC of a term set. Therefore, how to estimate the gene functional similarity reliably is still a challenging problem...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155659/grouping-mirnas-of-similar-functions-via-weighted-information-content-of-gene-ontology
#9
Chaowang Lan, Qingfeng Chen, Jinyan Li
BACKGROUND: Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited. This work introduces a computational method to group miRNAs of similar functions to identify co-regulating miRNAsfrom a similarity matrix of miRNAs. RESULTS: We define a novel information content of gene ontology (GO) to measure similarity between two sets of GO graphs corresponding to the two sets of target genes of two miRNAs...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28154822/enriching-genomic-resources-and-marker-development-from-transcript-sequences-of-jatropha-curcas-for-microgravity-studies
#10
Wenlan Tian, Dev Paudel, Wagner Vendrame, Jianping Wang
Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28145785/integrated-transcriptome-proteome-and-physiology-analysis-of-epinephelus-coioides-after-exposure-to-copper-nanoparticles-or-copper-sulfate
#11
Tao Wang, Xiaohua Long, Xiaoyan Chen, Yuanrui Liu, Zhaopu Liu, Shiqun Han, Shaohua Yan
Copper nanoparticles (Cu-NPs) are components in numerous commercial products, but little is known about the mechanisms of their toxicity to marine fish. Here, we investigated physiology, transcriptome and proteome in E. coioides after exposure to Cu as Cu-NPs or copper sulfate (CuSO4). Aggregation, oxidation and dissolution of Cu-NPs occurred after suspension in seawater within 24 h. Cu-NPs had similar types of the histology and hematological effects as CuSO4 on E. coioides, but toxicity of Cu-NPs seems more severe than that of CuSO4...
February 1, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/28145637/in-silico-identification-of-proteins-associated-with-drug-induced-liver-injury-based-on-the-prediction-of-drug-target-interactions
#12
Sergey Ivanov, Maxim Semin, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov
Drug-induced liver injury (DILI) is the leading cause of acute liver failure as well as one of the major reasons for drug withdrawal from clinical trials and the market. Elucidation of molecular interactions associated with DILI may help to detect potentially hazardous pharmacological agents at the early stages of drug development. The purpose of our study is to investigate which interactions with specific human protein targets may cause DILI. Prediction of interactions with 1534 human proteins was performed for the dataset with information about 699 drugs, which were divided into three categories of DILI: severe (178 drugs), moderate (310 drugs) and without DILI (211 drugs)...
February 1, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28129744/vitiligo-blood-transcriptomics-provides-new-insights-into-disease-mechanisms-and-identifies-potential-novel-therapeutic-targets
#13
Rama Dey-Rao, Animesh A Sinha
BACKGROUND: Significant gaps remain regarding the pathomechanisms underlying the autoimmune response in vitiligo (VL), where the loss of self-tolerance leads to the targeted killing of melanocytes. Specifically, there is incomplete information regarding alterations in the systemic environment that are relevant to the disease state. METHODS: We undertook a genome-wide profiling approach to examine gene expression in the peripheral blood of VL patients and healthy controls in the context of our previously published VL-skin gene expression profile...
January 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28126845/5-to-3-mrna-decay-contributes-to-the-regulation-of-arabidopsis-seed-germination-by-dormancy
#14
Isabelle Basbouss-Serhal, Stéphanie Pateyron, Juliette Leymarie, Francoise Cochet, Christophe Bailly
The regulation of plant gene expression, necessary for development and adaptive responses, does not rely only on RNA transcription but also on mRNA fate. To understand whether seed germination relies on the degradation of specific subsets of mRNA we investigated whether the 5' to 3' RNA decay machinery participated in the regulation of this process. Arabidopsis thaliana seeds of xrn4 (exoribonuclease4) and vcs (varicose) mutants displayed distinct dormancy phenotypes. Transcriptome analysis of xrn4-5 and vcs-8 mutant seeds allowed to identify genes which are likely to play a role in the control of germination...
January 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28116096/an-inhaled-dose-of-budesonide-induces-genes-involved-in-transcription-and-signaling-in-the-human-airways-enhancement-of-anti-and-proinflammatory-effector-genes
#15
Richard Leigh, Mahmoud M Mostafa, Elizabeth M King, Christopher F Rider, Suharsh Shah, Curtis Dumonceaux, Suzanne L Traves, Andrew McWhae, Tyler Kolisnik, Cora Kooi, Donna M Slater, Margaret M Kelly, Mark Bieda, Anna Miller-Larsson, Robert Newton
Although inhaled glucocorticoids, or corticosteroids (ICS), are generally effective in asthma, understanding their anti-inflammatory actions in vivo remains incomplete. To characterize glucocorticoid-induced modulation of gene expression in the human airways, we performed a randomized placebo-controlled crossover study in healthy male volunteers. Six hours after placebo or budesonide inhalation, whole blood, bronchial brushings, and endobronchial biopsies were collected. Microarray analysis of biopsy RNA, using stringent (≥2-fold, 5% false discovery rate) or less stringent (≥1...
August 2016: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28113907/alignment-of-ppi-networks-using-semantic-similarity-for-conserved-protein-complex-prediction
#16
Yong Shui, Young-Rae Cho
Network alignment is a computational technique to identify topological similarity of graph data by mapping link patterns. In bioinformatics, network alignment algorithms have been applied to protein-protein interaction (PPI) networks to discover evolutionarily conserved substructures at the system level. In particular, local network alignment of PPI networks searches for conserved functional components between species and predicts unknown protein complexes and signaling pathways. In this article, we present a novel approach of local network alignment by semantic mapping...
April 21, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28108505/comparative-transcriptomics-of-buzura-suppressaria-lepidoptera-geometridae-assembled-de-novo-yield-insights-into-response-after-buzura-suppressaria-nuclear-polyhedrosis-virus-infection
#17
Ji Luo, Yating Zhong, Jiyu Zhu, Guoying Zhou, Huayan Huang, Yaojun Wu
Buzura suppressaria Guenee (Lepidoptera: Geometridae) is a defoliator that seriously harms eucalyptus trees in South China. Buzura suppressaria nuclear polyhedrosis virus (BsNPV) is a baculovirus that infects B. suppressaria with high specificity and efficiency. Transcriptomes of B. suppressaria were sequenced before and after BsNPV infection using an Illumina-based platform to probe for differentially expressed genes (DEGs) of B. suppressaria after viral infection. On average, ∼57.4 million high-quality clean reads were generated and assembled de novo into 69,761 unigenes...
January 20, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#18
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Hong Seog Park, Seung-Hwan Park, Young-Su Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28101157/functional-analysis-of-keratinocyte-and-fibroblast-gene-expression-in-skin-and-keloid-scar-tissue-based-on-deviation-analysis-of-dynamic-capabilities
#19
Mingming Li, Lei Wu
The aim of the present study was to select key genes that are associated with fibroblasts and keratinocytes during keloid scar progression and development. The gene expression profile of GSE44270, which includes 32 samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in case samples compared with control samples were screened using the Limma R package followed by hierarchical clustering analysis. Protein-protein interaction (PPI) networks of the total selected DEGs were constructed using Cytoscape...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28089213/a-genome-wide-profiling-of-brain-dna-hydroxymethylation-in-alzheimer-s-disease
#20
Jinying Zhao, Yun Zhu, Jingyun Yang, Lin Li, Hao Wu, Philip L De Jager, Peng Jin, David A Bennett
INTRODUCTION: DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS: Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology...
January 6, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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