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Wgcna transcriptome

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https://www.readbyqxmd.com/read/29416627/transcriptome-evolution-from-breast-epithelial-cells-to-basal-like-tumors
#1
Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
In breast cancer, it is unclear the functional modifications at a transcriptomic level that are associated with the evolution from epithelial cells and ductal carcinoma in situ (DCIS) to basal-like tumors. By applying weighted gene co-expression network analysis (WGCNA), we identified 17 gene co-expression modules in normal, DCIS and basal-like tumor samples. We then correlated the expression pattern of these gene modules with disease progression from normal to basal-like tumours and found eight modules exhibiting a high and statistically significant correlation...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29410067/single-cell-transcriptome-analyses-reveal-molecular-signals-to-intrinsic-and-acquired-paclitaxel-resistance-in-esophageal-squamous-cancer-cells
#2
Hongjin Wu, Sean Chen, Charles Wang, Juehua Yu, Ying Li, Xiao-Yan Zhang, Ling Yang, Hongfang Zhang, Qiang Hou, Mingfeng Jiang, F Charles Brunicardi, Shixiu Wu
Paclitaxel is widely used in the combination chemotherapy for many cancers including esophageal squamous cell carcinoma (ESCC). However, the paclitaxel resistance occurs frequently in treating ESCC and the mechanism is not fully understood yet. The heterogeneity of gene expression within the drug-resistant cancer cells may be one of the major factors contributing to its resistance. In the present study, we successfully induced paclitaxel resistance in ESCC cell line KYSE-30 through low dose and long-term treatment of paclitaxel...
January 30, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29368590/identification-of-auxin-response-factor-gene-family-from-prunus-sibirica-and-its-expression-analysis-during-mesocarp-and-kernel-development
#3
Jun Niu, Quanxin Bi, Shuya Deng, Huiping Chen, Haiyan Yu, Libing Wang, Shanzhi Lin
BACKGROUND: Auxin response factors (ARFs) in auxin signaling pathway are an important component that can regulate the transcription of auxin-responsive genes involved in almost all aspects of plant growth and development. To our knowledge, the comprehensive and systematic characterization of ARF genes has never been reported in Prunus sibirica, a novel woody biodiesel feedstock in China. RESULTS: In this study, we identified 14 PsARF genes with a perfect open reading frame (ORF) in P...
January 24, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29335477/transcriptomic-signatures-of-cellular-and-humoral-immune-responses-in-older-adults-after-seasonal-influenza-vaccination-identified-by-data-driven-clustering
#4
Emily A Voigt, Diane E Grill, Michael T Zimmermann, Whitney L Simon, Inna G Ovsyannikova, Richard B Kennedy, Gregory A Poland
PBMC transcriptomes after influenza vaccination contain valuable information about factors affecting vaccine responses. However, distilling meaningful knowledge out of these complex datasets is often difficult and requires advanced data mining algorithms. We investigated the use of the data-driven Weighted Gene Correlation Network Analysis (WGCNA) gene clustering method to identify vaccine response-related genes in PBMC transcriptomic datasets collected from 138 healthy older adults (ages 50-74) before and after 2010-2011 seasonal trivalent influenza vaccination...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29281979/resistant-and-susceptible-chicken-lines-show-distinctive-responses-to-newcastle-disease-virus-infection-in-the-lung-transcriptome
#5
Melissa S Deist, Rodrigo A Gallardo, David A Bunn, Jack C M Dekkers, Huaijun Zhou, Susan J Lamont
BACKGROUND: Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-seq were studied using contrasts across the challenged and nonchallenged birds, the two lines, and three time points post-infection, and by using Weighted Gene Co-expression Network Analysis (WGNCA)...
December 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29280973/transcriptome-wide-identification-and-characterization-of-potato-circular-rnas-in-response-to-pectobacterium-carotovorum-subspecies-brasiliense-infection
#6
Ran Zhou, Yongxing Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Junliang Yin, Zhaohui Chu, Dongfang Ma
Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs...
December 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29196862/voluntary-exposure-to-a-toxin-the-genetic-influence-on-ethanol-consumption
#7
Paula L Hoffman, Laura M Saba, Lauren A Vanderlinden, Boris Tabakoff
Ethyl alcohol is a toxin that, when consumed at high levels, produces organ damage and death. One way to prevent or ameliorate this damage in humans is to reduce the exposure of organs to alcohol by reducing alcohol ingestion. Both the propensity to consume large volumes of alcohol and the susceptibility of human organs to alcohol-induced damage exhibit a strong genetic influence. We have developed an integrative genetic/genomic approach to identify transcriptional networks that predispose complex traits, including propensity for alcohol consumption and propensity for alcohol-induced organ damage...
December 1, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29189710/non-additive-transcriptomic-responses-to-inoculation-with-rhizobia-in-a-young-allopolyploid-compared-with-its-diploid-progenitors
#8
Adrian F Powell, Jeff J Doyle
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2...
November 30, 2017: Genes
https://www.readbyqxmd.com/read/29186495/sugar-metabolism-reprogramming-in-a-non-climacteric-bud-mutant-of-a-climacteric-plum-fruit-during-development-on-the-tree
#9
Macarena Farcuh, Bosheng Li, Rosa M Rivero, Lyudmila Shlizerman, Avi Sadka, Eduardo Blumwald
We investigated sugar metabolism in leaves and fruits of two Japanese plum (Prunus salicina Lindl.) cultivars, the climacteric Santa Rosa and its bud sport mutant the non-climacteric Sweet Miriam, during development on the tree. We previously characterized differences between the two cultivars. Here, we identified key sugar metabolic pathways. Pearson coefficient correlations of metabolomics and transcriptomic data and weighted gene co-expression network analysis (WGCNA) of RNA sequencing (RNA-Seq) data allowed the identification of 11 key sugar metabolism-associated genes: sucrose synthase, sucrose phosphate synthase, cytosolic invertase, vacuolar invertase, invertase inhibitor, α-galactosidase, β-galactosidase, galactokinase, trehalase, galactinol synthase, and raffinose synthase...
November 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29177853/bioinformatic-assessment-of-macrophage-activation-by-the-innate-immune-system
#10
Thomas Ulas, Joachim L Schultze, Marc Beyer
Weighted gene co-expression network analysis (WGCNA) allows for the identification and characterization of cell type-specific gene modules in complex transcriptome datasets. Here, we use a microarray dataset of human macrophages comprising 29 conditions and 299 samples generated by differentiation of CD14+ monocytes into macrophages followed by in vitro stimulations to identify stimulation-specific gene modules. These gene modules can be used for experimental validation, as well as further bioinformatic analysis to determine key pathways or upstream transcription factors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29166861/comprehensive-transcriptome-analysis-reveals-distinct-regulatory-programs-during-vernalization-and-floral-bud-development-of-orchardgrass-dactylis-glomerata-l
#11
Guangyan Feng, Linkai Huang, Ji Li, Jianping Wang, Lei Xu, Ling Pan, Xinxin Zhao, Xia Wang, Ting Huang, Xinquan Zhang
BACKGROUND: Vernalization and the transition from vegetative to reproductive growth involve multiple pathways, vital for controlling floral organ formation and flowering time. However, little transcription information is available about the mechanisms behind environmental adaption and growth regulation. Here, we used high-throughput sequencing to analyze the comprehensive transcriptome of Dactylis glomerata L. during six different growth periods. RESULTS: During vernalization, 4689 differentially expressed genes (DEGs) significantly increased in abundance, while 3841 decreased...
November 22, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29146547/a-gene-module-associated-with-dysregulated-tcr-signaling-pathways-in-cd4-t-cell-subsets-in-rheumatoid-arthritis
#12
Shuji Sumitomo, Yasuo Nagafuchi, Yumi Tsuchida, Haruka Tsuchiya, Mineto Ota, Kazuyoshi Ishigaki, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Norio Hanata, Shoko Tateishi, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Keishi Fujio, Kazuhiko Yamamoto
We analyzed the transcriptome of detailed CD4(+) T cell subsets including them after abatacept treatment, and examined the difference among CD4(+) T cell subsets and identified gene sets that are closely associated disease activity and abatacept treatment. Seven CD4(+) T cell subsets (naive, Th1, Th17, Th1/17, nonTh1/17, Tfh and Treg) were sorted from PBMCs taken from 10 RA patients and 10 healthy controls, and three RA patients donated samples before and 6 months after abatacept treatment. Paired-end RNA sequencing was performed using HiSeq 2500...
November 13, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29145611/identification-of-novel-potentially-pleiotropic-variants-associated-with-osteoporosis-and-obesity-using-cfdr-method
#13
Yuan Hu, Li-Jun Tan, Xiang-Ding Chen, Zhen Liu, Shi-Shi Min, Qin Zeng, Hui Shen, Hong-Wen Deng
Context: Genome-wide association studies (GWASs) have been successful in identifying loci associated with osteoporosis and obesity. However, the findings just explain a small fraction of the total genetic variance. Objective: The aim of this study was to identify novel pleiotropic genes important in osteoporosis and obesity. Design and Setting: A pleiotropic conditional false discovery rate (cFDR) method was applied to three independent GWAS summary statistics of femoral neck bone mineral density (FN BMD), body mass index (BMI) and waist-hip ratio (WHR)...
November 14, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29127223/systems-genetic-analysis-of-brown-adipose-tissue-function
#14
Michal Pravenec, Laura Saba, Vaclav Zidek, Vladimir Landa, Petr Mlejnek, Jan Silhavy, Miroslava Simakova, Hynak Strnad, Jaroslava Trnovska, Vojtech Skop, Martina Huttl, Irena Markova, Olena Oliyarnyk, Hana Malinska, Ludmila Kazdova, Harry Smith, Boris Tabakoff
Brown adipose tissue (BAT) has been suggested to play an important role in lipid and glucose metabolism in rodents and possibly also in humans. In the current study, we used genetic and correlation analyses in the BXH/HXB recombinant inbred (RI) strains, derived from Brown Norway (BN) and spontaneously hypertensive rats (SHR), to identify genetic determinants of BAT function. Linkage analyses revealed a quantitative trait locus (QTL) associated with interscapular BAT mass on chromosome 4 and two closely linked QTLs associated with glucose oxidation and glucose incorporation into BAT lipids on chromosome 2...
November 10, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/29115926/co-expression-network-analysis-of-the-transcriptomes-of-rice-roots-exposed-to-various-cadmium-stresses-reveals-universal-cadmium-responsive-genes
#15
Mingpu Tan, Dan Cheng, Yuening Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
BACKGROUND: The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. RESULTS: We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment...
November 7, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29025019/differing-molecular-response-of-young-and-advanced-maternal-age-human-oocytes-to-ivm
#16
J M Reyes, E Silva, J L Chitwood, W B Schoolcraft, R L Krisher, P J Ross
STUDY QUESTION: What effect does maternal age have on the human oocyte's molecular response to in vitro oocyte maturation? SUMMARY ANSWER: Although polyadenylated transcript abundance is similar between young and advanced maternal age (AMA) germinal vesicle (GV) oocytes, metaphase II (MII) oocytes exhibit a divergent transcriptome resulting from a differential response to in vitro oocyte maturation. WHAT IS KNOWN ALREADY: Microarray studies considering maternal age or maturation stage have shown that either of these factors will affect oocyte polyadenylated transcript abundance in human oocytes...
November 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28970079/human-kidney-tubule-specific-gene-expression-based-dissection-of-chronic-kidney-disease-traits
#17
Pazit Beckerman, Chengxiang Qiu, Jihwan Park, Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Sang-Youb Han, Peter Choi, Matthew Palmer, Katalin Susztak
Chronic kidney disease (CKD) has diverse phenotypic manifestations including structural (such as fibrosis) and functional (such as glomerular filtration rate and albuminuria) alterations. Gene expression profiling has recently gained popularity as an important new tool for precision medicine approaches. Here we used unbiased and directed approaches to understand how gene expression captures different CKD manifestations in patients with diabetic and hypertensive CKD. Transcriptome data from ninety-five microdissected human kidney samples with a range of demographics, functional and structural changes were used for the primary analysis...
October 2017: EBioMedicine
https://www.readbyqxmd.com/read/28912681/divergence-in-morris-water-maze-based-cognitive-performance-under-chronic-stress-is-associated-with-the-hippocampal-whole-transcriptomic-modification-in-mice
#18
Seung H Jung, Milene L Brownlow, Matteo Pellegrini, Ryan Jankord
Individual susceptibility determines the magnitude of stress effects on cognitive function. The hippocampus, a brain region of memory consolidation, is vulnerable to stressful environments, and the impact of stress on hippocampus may determine individual variability in cognitive performance. Therefore, the purpose of this study was to define the relationship between the divergence in spatial memory performance under chronically unpredictable stress and an associated transcriptomic alternation in hippocampus, the brain region of spatial memory consolidation...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28903352/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#19
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28886704/differentiated-transcriptional-signatures-in-the-maize-landraces-of-chiapas-mexico
#20
Matthew A Kost, Hugo R Perales, Saranga Wijeratne, Asela J Wijeratne, Eric Stockinger, Kristin L Mercer
BACKGROUND: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. RESULTS: Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico...
September 8, 2017: BMC Genomics
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