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Gene ontology, clustering

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https://www.readbyqxmd.com/read/28321951/transcriptional-network-analysis-in-frontal-cortex-in-lewy-body-diseases-with-focus-on-dementia-with-lewy-bodies
#1
Gabriel Santpere, Paula Garcia-Esparcia, Pol Andres-Benito, Belen Lorente-Galdos, Arcadi Navarro, Isidro Ferrer
The present study investigates global transcriptional changes in frontal cortex area 8 in incidental Lewy Body disease (iLBD), Parkinson disease (PD) and Dementia with Lewy bodies (DLB). We identified different co-expressed gene sets associated with disease stages, and gene ontology categories enriched in gene modules and differentially expressed genes including modules or gene clusters correlated to iLBD comprising upregulated dynein genes and taste receptors, and down-regulated innate inflammation. Focusing on DLB, we found modules with genes significantly enriched in functions related to RNA and DNA production, mitochondria and energy metabolism, purine metabolism, chaperone and protein folding system, and synapses and neurotransmission (particularly the GABAergic system)...
March 21, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28298526/the-ap-1-transcription-factor-c-jun-promotes-arthritis-by-regulating-cyclooxygenase-2-and-arginase-1-expression-in-macrophages
#2
Nicole Hannemann, Jutta Jordan, Sushmita Paul, Stephen Reid, Hanns-Wolf Baenkler, Sophia Sonnewald, Tobias Bäuerle, Julio Vera, Georg Schett, Aline Bozec
Activation of proinflammatory macrophages is associated with the inflammatory state of rheumatoid arthritis. Their polarization and activation are controlled by transcription factors such as NF-κB and the AP-1 transcription factor member c-Fos. Surprisingly, little is known about the role of the AP-1 transcription factor c-Jun in macrophage activation. In this study, we show that mRNA and protein levels of c-Jun are increased in macrophages following pro- or anti-inflammatory stimulations. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment cluster analyses of microarray data using wild-type and c-Jun-deleted macrophages highlight the central function of c-Jun in macrophages, in particular for immune responses, IL production, and hypoxia pathways...
March 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28298517/phosphoproteomics-of-fgf1-signaling-in-chondrocytes-identifying-the-signature-of-inhibitory-response
#3
Jessica R Chapman, Olga Katsara, Rachel Ruoff, David Morgenstern, Shruti Nayak, Claudio Basilico, Beatrix Ueberheide, Victoria Kolupaeva
Fibroblast growth factor (FGF) signaling is vital for many biological processes, beginning with development. The importance of FGF signaling for skeleton formation was first discovered by the analysis of genetic FGFR mutations which cause several bone morphogenetic disorders, including achondroplasia, the most common form of human dwarfism. The formation of the long bones is mediated through proliferation and differentiation of highly specialized cells - chondrocytes. Chondrocytes respond to FGF with growth inhibition, a unique response which differs from the proliferative response of the majority of cell types; however its molecular determinants are still unclear...
March 15, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28292312/comprehensive-discovery-of-subsample-gene-expression-components-by-information-explanation-therapeutic-implications-in-cancer
#4
Shirley Pepke, Greg Ver Steeg
BACKGROUND: De novo inference of clinically relevant gene function relationships from tumor RNA-seq remains a challenging task. Current methods typically either partition patient samples into a few subtypes or rely upon analysis of pairwise gene correlations that will miss some groups in noisy data. Leveraging higher dimensional information can be expected to increase the power to discern targetable pathways, but this is commonly thought to be an intractable computational problem. METHODS: In this work we adapt a recently developed machine learning algorithm for sensitive detection of complex gene relationships...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28286417/molecular-mechanism-of-g1-arrest-and-cellular-senescence-induced-by-lee011-a-novel-cdk4-cdk6-inhibitor-in-leukemia-cells
#5
Yan-Fang Tao, Na-Na Wang, Li-Xiao Xu, Zhi-Heng Li, Xiao-Lu Li, Yun-Yun Xu, Fang Fang, Mei Li, Guang-Hui Qian, Yan-Hong Li, Yi-Ping Li, Yi Wu, Jun-Li Ren, Wei-Wei Du, Jun Lu, Xing Feng, Jian Wang, Wei-Qi He, Shao-Yan Hu, Jian Pan
BACKGROUND: Overexpression of cyclin D1 dependent kinases 4 and 6 (CDK4/6) is a common feature of many human cancers including leukemia. LEE011 is a novel inhibitor of both CDK4 and 6. To date, the molecular function of LEE011 in leukemia remains unclear. METHODS: Leukemia cell growth and apoptosis following LEE011 treatment was assessed through CCK-8 and annexin V/propidium iodide staining assays. Cell senescence was assessed by β-galactosidase staining and p16(INK4a) expression analysis...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28282934/alternative-splicing-profile-and-sex-preferential-gene-expression-in-the-female-and-male-pacific-abalone-haliotis-discus-hannai
#6
Mi Ae Kim, Jae-Sung Rhee, Tae Ha Kim, Jung Sick Lee, Ah-Young Choi, Beom-Soon Choi, Ik-Young Choi, Young Chang Sohn
In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively...
March 9, 2017: Genes
https://www.readbyqxmd.com/read/28281648/proteomic-analysis-of-host-cell-protein-dynamics-in-the-culture-supernatants-of-antibody-producing-cho-cells
#7
Jin Hyoung Park, Jong Hwa Jin, Myung Sin Lim, Hyun Joo An, Jong Won Kim, Gyun Min Lee
Chinese hamster ovary (CHO) cells are the most common cell line used for the production of therapeutic proteins including monoclonal antibodies (mAbs). Host cell proteins (HCPs), secreted and released from lysed cells, accumulate extracellularly during the cultures of recombinant CHO (rCHO) cells, potentially impairing product quality. In an effort to maintain good mAb quality during the cultures, HCPs accumulated extracellularly in batch and fed-batch cultures of a mAb-producing rCHO cell line were identified and quantified by nanoflow liquid chromatography-tandem mass spectrometry, followed by their gene ontology and functional analysis...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28260076/gene-expression-profiles-reveal-key-pathways-and-genes-associated-with-neuropathic-pain-in-patients-with-spinal-cord-injury
#8
Xijing He, Liying Fan, Zhongheng Wu, Jiaxuan He, Bin Cheng
Previous gene expression profiling studies of neuropathic pain (NP) following spinal cord injury (SCI) have predominantly been performed in animal models. The present study aimed to investigate gene alterations in patients with spinal cord injury and to further examine the mechanisms underlying NP following SCI. The GSE69901 gene expression profile was downloaded from the public Gene Expression Omnibus database. Samples of peripheral blood mononuclear cells (PBMCs) derived from 12 patients with intractable NP and 13 control patients without pain were analyzed to identify the differentially expressed genes (DEGs), followed by functional enrichment analysis and protein‑protein interaction (PPI) network construction...
February 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28259986/identification-of-key-genes-and-pathways-associated-with-spinal-cord-injury
#9
Yue-Hui Zhang, Jia Song, Li-Gang Wang, Jiang Shao
The present study was designed to identify key genes or significant signaling pathways associated with spinal cord injury (SCI), and to clarify the underlying molecular mechanisms of SCI. Data from the GSE45550 array were downloaded from the Gene Expression Omnibus database. A total of 6 control samples, 6 samples at 3 days post‑SCI (SCI3d), 6 samples at 8 days post‑SCI (SCI8d) and 6 samples at 14 days post‑SCI (SCI14d) were included. The microarray data was preprocessed by the robust multi‑array average algorithm...
February 10, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28253086/oocyte-developmental-competence-insights-from-cross-species-differential-gene-expression-and-human-oocyte-specific-functional-gene-networks
#10
Fernando H Biase
Understanding oocyte developmental competence remains a key challenge for reproductive biology and systems sciences. The transcriptome of oocytes in eutherians is highly complex and is associated with the success of embryo development. Due to sample limitations from humans, animal models are used for investigation of the oocyte transcriptome. Nonetheless, little is known about the diversity of the oocyte transcriptome across eutherians. In this report, comprehensive investigation of 7 public data sets in 4 species, human, macaque, mice, and cattle, shows that 16,572 genes are expressed in oocytes...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28250580/genome-wide-identification-and-comparative-expression-analysis-of-lea-genes-in-watermelon-and-melon-genomes
#11
Yasemin Celik Altunoglu, Mehmet Cengiz Baloglu, Pinar Baloglu, Esra Nurten Yer, Sibel Kara
Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study...
January 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/28241786/de-novo-sequencing-and-comparative-transcriptome-analysis-of-the-male-and-hermaphroditic-flowers-provide-insights-into-the-regulation-of-flower-formation-in-andromonoecious-taihangia-rupestris
#12
Weiguo Li, Lihui Zhang, Zhan Ding, Guodong Wang, Yandi Zhang, Hongmei Gong, Tianjun Chang, Yanwen Zhang
BACKGROUND: Taihangia rupestris, an andromonoecious plant species, bears both male and hermaphroditic flowers within the same individual. However, the establishment and development of male and hermaphroditic flowers in andromonoecious Taihangia remain poorly understood, due to the limited genetic and sequence information. To investigate the potential molecular mechanism in the regulation of Taihangia flower formation, we used de novo RNA sequencing to compare the transcriptome profiles of male and hermaphroditic flowers at early and late developmental stages...
February 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28239355/modification-of-flight-and-locomotion-performances-respiratory-metabolism-and-transcriptome-expression-in-the-lady-beetle-harmonia-axyridis-through-sublethal-pesticide-exposure
#13
Da Xiao, Xiaoling Tan, Wenjuan Wang, Fan Zhang, Nicolas Desneux, Su Wang
Biological control is usually used in combination with chemical control for practical agricultural applications. Thus, the influence of insecticides on the natural predators used for biological control should be investigated for integrated pest management. The ladybird Harmonia axyridis is an effective predator on aphids and coccids. Beta-cypermethrin is a broad-spectrum insecticide used worldwide for controlling insect pests. H. axyridis is becoming increasingly threatened by this insecticide. Here, we investigated the effect of a sublethal dose of beta-cypermethrin on flight, locomotion, respiration, and detoxification system of H...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28239339/microarray-and-qpcr-analyses-of-wallerian-degeneration-in-rat-sciatic-nerves
#14
Sheng Yi, Xin Tang, Jun Yu, Jie Liu, Fei Ding, Xiaosong Gu
Wallerian degeneration occurs immediately following injury to mammal peripheral nerves. To better understand the molecular events occurring during Wallerian degeneration, a rat model of sciatic nerve transection was used to assess differentially expressed genes at 0.5, 1, 6, 12, 24 h, 4 days, 1, 2, 3, and 4 weeks post nerve injury (PNI). Hierarchical clustering, Euclidean distance matrix, and principal component analysis (PCA) collectively suggested three distinct phases within the post-injury period of 4 weeks...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28229116/short-and-long-term-changes-in-sugarbeet-beta-vulgaris-l-gene-expression-due-to-postharvest-jasmonic-acid-treatment-data
#15
Lucilene Silva de Oliveira, Karen Klotz Fugate, Jocleita Perruzo Ferrareze, Melvin D Bolton, Edward L Deckard, Fernando L Finger
Jasmonic acid is a natural plant hormone that induces native defense responses in plants. Sugarbeet (Beta vulgaris L.) root unigenes that were differentially expressed 2 and 60 days after a postharvest jasmonic acid treatment are presented. Data include changes in unigene expression relative to water-treated controls, unigene annotations against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and unigene annotations with Gene Ontology (GO) terms...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28222107/transcriptional-response-to-131i-exposure-of-rat-thyroid-gland
#16
Nils Rudqvist, Johan Spetz, Emil Schüler, Toshima Z Parris, Britta Langen, Khalil Helou, Eva Forssell-Aronsson
Humans are exposed to 131I in medical diagnostics and treatment but also from nuclear accidents, and better knowledge of the molecular response in thyroid is needed. The aim of the study was to examine the transcriptional response in thyroid tissue 24 h after 131I administration in rats. The exposure levels were chosen to simulate both the clinical situation and the case of nuclear fallout. Thirty-six male rats were i.v. injected with 0-4700 kBq 131I, and killed at 24 h after injection (Dthyroid = 0.0058-3...
2017: PloS One
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
#17
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
#18
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
#19
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
#20
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
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