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Gene ontology, clustering

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https://www.readbyqxmd.com/read/28545501/pregnancy-induced-gene-expression-changes-in-vivo-among-women-with-rheumatoid-arthritis-a-pilot-study
#1
Dana E Goin, Mette Kiel Smed, Lior Pachter, Elizabeth Purdom, J Lee Nelson, Hanne Kjærgaard, Jørn Olsen, Merete Lund Hetland, Vibeke Zoffmann, Bent Ottesen, Damini Jawaheer
BACKGROUND: Little is known about gene expression changes induced by pregnancy in women with rheumatoid arthritis (RA) and healthy women because the few studies previously conducted did not have pre-pregnancy samples available as baseline. We have established a cohort of women with RA and healthy women followed prospectively from a pre-pregnancy baseline. In this study, we tested the hypothesis that pregnancy-induced changes in gene expression among women with RA who improve during pregnancy (pregDASimproved) overlap substantially with changes observed among healthy women and differ from changes observed among women with RA who worsen during pregnancy (pregDASworse)...
May 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28542579/transcriptomic-dissection-reveals-wide-spread-differential-expression-in-chickpea-during-early-time-points-of-fusarium-oxysporum-f-sp-ciceri-race-1-attack
#2
Sumanti Gupta, Anirban Bhar, Moniya Chatterjee, Amartya Ghosh, Sampa Das
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f...
2017: PloS One
https://www.readbyqxmd.com/read/28541580/genes-and-gene-clusters-related-to-genotype-and-drought-induced-variation-in-saccharification-potential-lignin-content-and-wood-anatomical-traits-in-populus-nigra%C3%A2
#3
Henning Wildhagen, Shanty Paul, Mike Allwright, Hazel K Smith, Marta Malinowska, Sabine K Schnabel, M João Paulo, Federica Cattonaro, Vera Vendramin, Simone Scalabrin, Dennis Janz, Cyril Douthe, Oliver Brendel, Cyril Buré, David Cohen, Irène Hummel, Didier Le Thiec, Fred van Eeuwijk, Joost J B Keurentjes, Jaume Flexas, Michele Morgante, Paul Robson, Marie-Béatrice Bogeat-Triboulot, Gail Taylor, Andrea Polle
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential...
May 24, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28534985/microarray-analysis-of-differentially-expressed-genes-in-l929-mouse-fibroblast-cells-exposed-to-leptin-and-hypoxia
#4
Ping Ouyang, Sen Wang, He Zhang, Zhigang Huang, Pei Wei, Ye Zhang, Zhuguo Wu, Tao Li
Leptin and hypoxia are pro-fibrotic factors involved in fibrogenesis, however, the gene expression profiles remain to be fully elucidated. The aim of the present study was to investigate the regulatory roles of leptin and hypoxia on the L929 mouse fibroblast cell line. The cells were assigned to a normoxia, normoxia with leptin, hypoxia, and hypoxia with leptin group. The cDNA expression was detected using an Agilent mRNA array platform. The differentially expressed genes (DEGs) in response to leptin and hypoxia were identified using reverse transcription‑quantitative polymerase chain reaction analysis, followed by clustering analysis, Gene Ontology analysis and pathway analysis...
May 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28525976/the-adaptation-of-colorectal-cancer-cells-when-forming-metastases-in-the-liver-expression-of-associated-genes-and-pathways-in-a-mouse-model
#5
Derya Bocuk, Alexander Wolff, Petra Krause, Gabriela Salinas, Annalen Bleckmann, Christina Hackl, Tim Beissbarth, Sarah Koenig
BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related death in men and women. Systemic disease with metastatic spread to distant sites such as the liver reduces the survival rate considerably. The aim of this study was to investigate the changes in gene expression that occur on invasion and expansion of CRC cells when forming metastases in the liver. METHODS: The livers of syngeneic C57BL/6NCrl mice were inoculated with 1 million CRC cells (CMT-93) via the portal vein, leading to the stable formation of metastases within 4 weeks...
May 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28523007/transcriptomic-identification-of-drought-related-genes-and-ssr-markers-in-sudan-grass-based-on-rna-seq
#6
Yongqun Zhu, Xia Wang, Linkai Huang, Chaowen Lin, Xinquan Zhang, Wenzhi Xu, Jianhua Peng, Zhou Li, Haidong Yan, Fuxiang Luo, Xie Wang, Li Yao, Dandan Peng
Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28511992/rna-seq-analyses-reveal-that-cervical-spinal-cords-and-anterior-motor-neurons-from-amyotrophic-lateral-sclerosis-subjects-show-reduced-expression-of-mitochondrial-dna-encoded-respiratory-genes-and-rhtfam-may-correct-this-respiratory-deficiency
#7
Amy C Ladd, David G Brohawn, Ravindar R Thomas, Paula M Keeney, Stuart S Berr, Shaharyar M Khan, Francisco R Portell, Meiram Zh Shakenov, Patrick F Antkowiak, Bijoy Kundu, Nicholas Tustison, James P Bennett
Amyotrophic lateral sclerosis (ALS) is a generally fatal neurodegenerative disease of adults that produces weakness and atrophy due to dysfunction and death of upper and lower motor neurons. We used RNA-sequencing (RNA-seq) to analyze expression of all mitochondrial DNA (mtDNA)-encoded respiratory genes in ALS and CTL human cervical spinal cords (hCSC) and isolated motor neurons. We analyzed with RNA-seq mtDNA gene expression in human neural stem cells (hNSC) exposed to recombinant human mitochondrial transcription factor A (rhTFAM), visualized in 3-dimensions clustered gene networks activated by rhTFAM, quantitated their interactions with other genes and determined their gene ontology (GO) families...
May 13, 2017: Brain Research
https://www.readbyqxmd.com/read/28501396/analysis-of-copy-number-variations-in-holstein-friesian-cow-genomes-based-on-whole-genome-sequence-data
#8
M Mielczarek, M Frąszczak, R Giannico, G Minozzi, John L Williams, K Wojdak-Maksymiec, J Szyda
Thirty-two whole genome DNA sequences of cows were analyzed to evaluate inter-individual variability in the distribution and length of copy number variations (CNV) and to functionally annotate CNV breakpoints. The total number of deletions per individual varied between 9,731 and 15,051, whereas the number of duplications was between 1,694 and 5,187. Most of the deletions (81%) and duplications (86%) were unique to a single cow. No relation between the pattern of variant sharing and a family relationship or disease status was found...
May 10, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28500632/altered-expression-of-four-mirna-mir-1238-3p-mir-202-3p-mir-630-and-mir-766-3p-and-their-potential-targets-in-peripheral-blood-from-vitiligo-patients
#9
Zhiwei Shang, Hongwen Li
Vitiligo is an acquired skin disease with pigmentary disorder. Autoimmune destruction of melanocytes is thought to be major factor in the etiology of vitiligo. miRNA-based regulators of gene expression have been reported to play crucial roles in autoimmune disease. Therefore, we attempt to profile the miRNA expressions and predict their potential targets, assessing the biological functions of differentially expressed miRNA. Total RNA was extracted from peripheral blood of vitiligo (experimental group, n = 5) and non-vitiligo (control group, n = 5) age-matched patients...
May 13, 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28499413/ranking-metrics-in-gene-set-enrichment-analysis-do-they-matter
#10
Joanna Zyla, Michal Marczyk, January Weiner, Joanna Polanska
BACKGROUND: There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. METHODS AND RESULTS: In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28479385/digital-gene-expression-profiling-of-flax-linum-usitatissimum-l-stem-peel-identifies-genes-enriched-in-fiber-bearing-phloem-tissue
#11
Yuan Guo, Caisheng Qiu, Songhua Long, Ping Chen, Dongmei Hao, Marta Preisner, Hui Wang, Yufu Wang
To better understand the molecular mechanisms and gene expression characteristics associated with development of bast fiber cell within flax stem phloem, the gene expression profiling of flax stem peels and leaves were screened, using Illumina's Digital Gene Expression (DGE) analysis. Four DGE libraries (2 for stem peel and 2 for leaf), ranging from 6.7 to 9.2 million clean reads were obtained, which produced 7.0 million and 6.8 million mapped reads for flax stem peel and leave, respectively. By differential gene expression analysis, a total of 975 genes, of which 708 (73%) genes have protein-coding annotation, were identified as phloem enriched genes putatively involved in the processes of polysaccharide and cell wall metabolism...
May 4, 2017: Gene
https://www.readbyqxmd.com/read/28476666/label-free-proteomic-analysis-of-intestinal-mucosa-proteins-in-common-carp-cyprinus-carpio-infected-with-aeromonas-hydrophila
#12
Guilan Di, Hui Li, Chao Zhang, Yanjing Zhao, Chuanjiang Zhou, Sajid Naeem, Li Li, Xianghui Kong
Outbreaks of infectious diseases in common carp Cyprinus carpio, a major cultured fish in northern regions of China, constantly result in significant economic losses. Until now, information proteomic on immune defence remains limited. In the present study, a profile of intestinal mucosa immune response in Cyprinus carpio was investigated after 0, 12, 36 and 84 h after challenging tissues with Aeromonas hydrophila at a concentration of 1.4 × 10(8) CFU/mL. Proteomic profiles in different samples were compared using label-free quantitative proteomic approach...
May 3, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28476633/dna-methylation-in-lung-tissues-of-mouse-offspring-exposed-in-utero-to-polycyclic-aromatic-hydrocarbons
#13
Trevor J Fish, Abby D Benninghoff
Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and are suspected lung carcinogens in humans. Moreover, evidence from cell-based studies points to PAHs as modulators of the epigenome. The objective of this work was to assess patterns of genome-wide DNA methylation in lung tissues of adult offspring initiated in utero with the transplacental PAH carcinogens dibenzo [def,p]chrysene (DBC) or benzo [a]pyrene (BaP). Genome-wide methylation patterns for normal (not exposed), normal adjacent and lung tumor tissues obtained from adult offspring were determined using methylated DNA immunoprecipitation (MeDIP) with the NimbleGen mouse DNA methylation CpG island array...
May 2, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28460117/fast-genome-wide-functional-annotation-through-orthology-assignment-by-eggnog-mapper
#14
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g. new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. We therefore developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database...
April 29, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28455229/itraq-quantitative-proteomic-study-in-patients-with-thoracic-ossification-of-the-ligamentum-flavum
#15
Bingxiang Wang, Zhongqiang Chen, Xiangyu Meng, Mengtao Li, Xiaoxi Yang, Chi Zhang
Thoracic ossification of the ligamentum flavum (TOLF) is a unique disease with ectopic ossification, and is a major cause of thoracic spinal stenosis and myelopathy. However, the underlying etiology remains largely unknown. In this study, the ligamentum flavum was systematically analyzed in TOLF patients by using comprehensive iTRAQ labeled quantitative proteomics. Among 1285 detected proteins, there were 282 proteins identified to be differentially expressed. The Gene Ontology (GO) analysis regarding functional annotation of proteins consists of the following three aspects: the biological process, the molecular function, and the cellular components...
June 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28439089/transcriptome-analysis-on-the-exoskeleton-formation-in-early-developmetal-stages-and-reconstruction-scenario-in-growth-moulting-in-litopenaeus-vannamei
#16
Yi Gao, Jiankai Wei, Jianbo Yuan, Xiaojun Zhang, Fuhua Li, Jianhai Xiang
Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429739/a-large-scale-benchmark-of-gene-prioritization-methods
#17
Dimitri Guala, Erik L L Sonnhammer
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#18
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421658/transcriptional-signatures-of-connectomic-subregions-of-the-human-striatum
#19
Linden Parkes, Ben Fulcher, Murat Yücel, Alex Fornito
Functionally distinct regions of the brain are thought to possess a characteristic connectional fingerprint - a profile of incoming and outgoing connections that defines the function of that area. This observation has motivated efforts to subdivide brain areas using their connectivity patterns. However, it remains unclear whether these connectomically-defined subregions can be distinguished at the molecular level. Here, we combine high-resolution diffusion-weighted magnetic resonance imaging with transcriptomic data to show that connectomically-defined subregions of the striatum carry distinct transcriptional signatures...
April 19, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28420359/saikosaponins-induced-hepatotoxicity-in-mice-via-lipid-metabolism-dysregulation-and-oxidative-stress-a-proteomic-study
#20
Xiaoyu Li, Xiaojiaoyang Li, Junxian Lu, Youyi Huang, Lili Lv, Yongfu Luan, Runping Liu, Rong Sun
BACKGROUND: Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury. METHODS: Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice...
April 19, 2017: BMC Complementary and Alternative Medicine
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