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Gene ontology, clustering

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https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#1
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27899966/analysis-of-the-molecular-mechanism-of-osteosarcoma-using-a-bioinformatics-approach
#2
Jianxun Yang, Ning Wang
The aim of this study was to explore the underlying molecular mechanism related to the process and progression of osteosarcoma (OS). The differentially expressed genes (DEGs) were downloaded from the Gene Expression Omnibus database. The pathway and gene ontology (GO) enrichment analysis, as well as transcription factor, tumor-associated gene and tumor suppressor gene analyses were performed to investigate the functions of DEGs. Next, the protein-protein interaction (PPI) network was constructed and module analysis was further assessed by cluster analysis with the overlapping neighborhood expansion (Cluster ONE) cytoscape plug-in...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27898811/de-novo-transcriptome-assembly-and-dynamic-spatial-gene-expression-analysis-in-red-clover
#3
Manohar Chakrabarti, Randy D Dinkins, Arthur G Hunt
Red clover ( L.) is a cool-season forage legume grown throughout the northeastern United States and is the most widely planted forage legume after alfalfa ( L.). Red clover provides high-value feed to the livestock because of high protein content and easy digestibility. To date, genomic resources for red clover are scarce. In the current study, a de novo transcriptome assembly of red clover was constructed representing different tissue types. The draft assembly consists of 37,565 contigs with N50 and average contig length of 1707 and 1262 bp, respectively...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27896963/exploring-brain-transcriptomic-patterns-a-topological-analysis-using-spatial-expression-networks
#4
Zhana Kuncheva, Michelle L Krishnan, Giovanni Montana
Characterizing the transcriptome architecture of the human brain is fundamental in gaining an understanding of brain function and disease. A number of recent studies have investigated patterns of brain gene expression obtained from an extensive anatomical coverage across the entire human brain using experimental data generated by the Allen Human Brain Atlas (AHBA) project. In this paper, we propose a new representation of a gene's transcription activity that explicitly captures the pattern of spatial co-expression across different anatomical brain regions...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27893688/identification-of-genes-and-signaling-pathways-associated-with-diabetic-neuropathy-using-a-weighted-correlation-network-analysis-a-consort-study
#5
Ya Li, Weiguo Ma, Chuanqing Xie, Min Zhang, Xiaohong Yin, Fenfen Wang, Jie Xu, Bingyin Shi
BACKGROUND: The molecular mechanisms behind diabetic neuropathy remains to be investigated. METHODS: This is a secondary study on microarray dataset (GSE24290) downloaded from Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI), which included 18 nerve tissue samples of progressing diabetic neuropathy (fibers loss ≥500 fibers/mm) and 17 nerve tissue samples of nonprogressing diabetic neuropathy (fibers loss ≤100 fibers/mm)...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27885528/a-network-biology-approach-to-understanding-the-importance-of-chameleon-proteins-in-human-physiology-and-pathology
#6
Golnaz Bahramali, Bahram Goliaei, Zarrin Minuchehr, Sayed-Amir Marashi
Chameleon proteins are proteins which include sequences that can adopt α-helix-β-strand (HE-chameleon) or α-helix-coil (HC-chameleon) or β-strand-coil (CE-chameleon) structures to operate their crucial biological functions. In this study, using a network-based approach, we examined the chameleon proteins to give a better knowledge on these proteins. We focused on proteins with identical chameleon sequences with more than or equal to seven residues long in different PDB entries, which adopt HE-chameleon, HC-chameleon, and CE-chameleon structures in the same protein...
November 24, 2016: Amino Acids
https://www.readbyqxmd.com/read/27871313/conservation-of-immune-gene-signatures-in-solid-tumors-and-prognostic-implications
#7
Julia Chifman, Ashok Pullikuth, Jeff W Chou, Davide Bedognetti, Lance D Miller
BACKGROUND: Tumor-infiltrating leukocytes can either limit cancer growth or facilitate its spread. Diagnostic strategies that comprehensively assess the functional complexity of tumor immune infiltrates could have wide-reaching clinical value. In previous work we identified distinct immune gene signatures in breast tumors that reflect the relative abundance of infiltrating immune cells and exhibited significant associations with patient outcomes. Here we hypothesized that immune gene signatures agnostic to tumor type can be identified by de novo discovery of gene clusters enriched for immunological functions and possessing internal correlation structure conserved across solid tumors from different anatomic sites...
November 22, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27806724/a-network-pathway-based-module-identification-for-predicting-the-prognosis-of-ovarian-cancer-patients
#8
Xin Wang, Shan-Shan Wang, Lin Zhou, Li Yu, Lan-Mei Zhang
BACKGROUND: This study aimed to screen multiple genes biomarkers based on gene expression data for predicting the survival of ovarian cancer patients. METHODS: Two microarray data of ovarian cancer samples were collected from The Cancer Genome Atlas (TCGA) database. The data in the training set were used to construct Reactome functional interactions network, which then underwent Markov clustering, supervised principal components, Cox proportional hazard model to screen significantly prognosis related modules...
November 2, 2016: Journal of Ovarian Research
https://www.readbyqxmd.com/read/27796151/cell-cycle-m-phase-genes-are-highly-upregulated-in-anaplastic-thyroid-carcinoma
#9
Paul Weinberger, Sithara Raju Ponny, Hongyan Xu, Shan Bai, Robert C Smallridge, John A Copland, Ashok Sharma
<b>Background:</b> Anaplastic thyroid carcinoma (ATC) accounts for only 3% of thyroid cancers, yet strikingly it accounts for almost 40% of thyroid cancer deaths. Currently, no effective therapies exist. In an effort to identify ATC-specific therapeutic targets, we analyzed global gene expression data from multiple studies to identify ATC specific dysregulated genes. <b>Methods:</b> The NCBI Gene Expression Omnibus database was searched for high-throughput gene expression microarray studies from human ATC tissue along with normal thyroid and/or papillary thyroid cancer (PTC) tissue...
October 31, 2016: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/27791988/dysregulated-expression-of-micrornas-and-mrnas-in-pulmonary-artery-remodeling-in-ascites-syndrome-in-broiler-chickens
#10
Ping Liu, Fei Yang, Yu Zhuang, Qingyang Xiao, Huabin Cao, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Xiaoquan Guo, Guoliang Hu
Ascites syndrome (AS), also known as pulmonary artery hypertension, remains a challenging disease that severely affects both humans and broiler chickens. Pulmonary artery remodeling presents a key step in the development of AS. In this study, we obtained pulmonary artery tissues from broilers with and without AS to perform miRNA sequencing analysis, miRNA-mRNA association analysis and pathological examinations. 29 significantly differentially expressed miRNAs were found both in known and novel miRNAs with 18 up-regulated and 11 down-regulated miRNAs...
October 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27789186/novel-gene-brain-structure-relationships-in-psychotic-disorder-revealed-using-parallel-independent-component-analyses
#11
Neeraj Tandon, Pranav Nanda, Jaya L Padmanabhan, Ian T Mathew, Shaun M Eack, Balaji Narayanan, Shashwath A Meda, Sarah E Bergen, Gualbert Ruaño, Andreas Windemuth, Mohan Kocherla, Tracey L Petryshen, Brett Clementz, John Sweeney, Carol Tamminga, Godfrey Pearlson, Matcheri S Keshavan
BACKGROUND: Schizophrenia, schizoaffective disorder, and psychotic bipolar disorder overlap with regard to symptoms, structural and functional brain abnormalities, and genetic risk factors. Neurobiological pathways connecting genes to clinical phenotypes across the spectrum from schizophrenia to psychotic bipolar disorder remain largely unknown. METHODS: We examined the relationship between structural brain changes and risk alleles across the psychosis spectrum in the multi-site Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) cohort...
October 24, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27770355/meta-analysis-of-genome-wide-chromatin-data
#12
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
https://www.readbyqxmd.com/read/27768772/de-novo-transcriptomes-of-forsythia-koreana-using-a-novel-assembly-method-insight-into-tissue-and-species-specific-expression-of-lignan-biosynthesis-related-gene
#13
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
https://www.readbyqxmd.com/read/27756219/gene-expression-profile-indicates-involvement-of-no-in-camellia-sinensis-pollen-tube-growth-at-low-temperature
#14
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
https://www.readbyqxmd.com/read/27748870/identification-of-therapeutic-targets-for-alzheimer-s-disease-via-differentially-expressed-gene-and-weighted-gene-co-expression-network-analyses
#15
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
https://www.readbyqxmd.com/read/27742864/deep-rna-sequencing-analysis-of-syncytialization-related-genes-during-bewo-cell-fusion
#16
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
https://www.readbyqxmd.com/read/27720830/transcriptome-analysis-of-the-responses-to-methyl-methanesulfonate-treatment-in-mouse-pachytene-spermatocytes-and-round-spermatids
#17
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
https://www.readbyqxmd.com/read/27718328/rna-seq-identifies-redox-balance-related-gene-expression-alterations-under-acute-cadmium-exposure-in-yeast
#18
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
https://www.readbyqxmd.com/read/27713521/transcriptome-comparison-analysis-of-ostrinia-furnacalis-in-four-developmental-stages
#19
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
https://www.readbyqxmd.com/read/27709374/exploring-drought-stress-regulated-genes-in-senna-cassia-angustifolia-vahl-a-transcriptomic-approach
#20
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
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