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gene set enrichment

Weijie Zhang, Zhimeng Lv, Chenghua Li, Yahui Sun, Huijie Jiang, Manxi Zhao, Xuelin Zhao, Yina Shao, Yaqing Chang
Spotting disease is a common disease in the process of aquaculture and restocking of the sea urchin Strongylocentrotus intermedius and leads to mass mortality. To characterize the molecular processes and candidate genes related to spotting disease in S. intermedius, we conducted next-generation sequencing to assess the key genes/pathways in spotting diseased sea urchin (DUG) compared to healthy ones (HUG). A total of 321.1 million clean reads were obtained and assembled into 93,877 Unigenes with an N50 of 1185 bp, in which 86...
October 17, 2018: Fish & Shellfish Immunology
Mareen Matz, Frederik Heinrich, Qiang Zhang, Christine Lorkowski, Evelyn Seelow, Kaiyin Wu, Nils Lachmann, Richard Kwasi Addo, Pawel Durek, Mir-Farzin Mashreghi, Klemens Budde
CONTEXT: Antibody-mediated rejection (ABMR) after kidney transplantation (KTx) remains the crucial obstacle to successful long-term graft function. The identification of gene signatures involved in ABMR could grant the basis for better prevention and treatment strategies. OBJECTIVE: The identification of gene signatures in whole blood cells specific for ABMR after kidney transplantation. MATERIAL AND METHODS: Total RNA from blood cells of 16 kidney transplanted patients with ABMR, stable graft function (SGF) and with T-cell mediated rejection (TCMR) was isolated...
October 20, 2018: Clinical Transplantation
Xiang Zhu, Matthew Stephens
Genome-wide association studies (GWAS) aim to identify genetic factors associated with phenotypes. Standard analyses test variants for associations individually. However, variant-level associations are hard to identify and can be difficult to interpret biologically. Enrichment analyses help address both problems by targeting sets of biologically related variants. Here we introduce a new model-based enrichment method that requires only GWAS summary statistics. Applying this method to interrogate 4,026 gene sets in 31 human phenotypes identifies many previously-unreported enrichments, including enrichments of endochondral ossification pathway for height, NFAT-dependent transcription pathway for rheumatoid arthritis, brain-related genes for coronary artery disease, and liver-related genes for Alzheimer's disease...
October 19, 2018: Nature Communications
Anand Mayakonda, De-Chen Lin, Yassen Assenov, Christoph Plass, H Phillip Koeffler
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from somatic mutations entails a number of computational and statistical approaches, requiring usage of independent software and numerous tools. Here, we describe an R Bioconductor package, Maftools, which offers a multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses...
October 19, 2018: Genome Research
Ruth Alexandra Stoney, Jean-Marc Schwartz, David L Robertson, Goran Nenadic
BACKGROUND: The consolidation of pathway databases, such as KEGG, Reactome and ConsensusPathDB, has generated widespread biological interest, however the issue of pathway redundancy impedes the use of these consolidated datasets. Attempts to reduce this redundancy have focused on visualizing pathway overlap or merging pathways, but the resulting pathways may be of heterogeneous sizes and cover multiple biological functions. Efforts have also been made to deal with redundancy in pathway data by consolidating enriched pathways into a number of clusters or concepts...
October 19, 2018: BMC Bioinformatics
Elham Khodayari Moez, Saumyadipta Pyne, Irina Dinu
BACKGROUND: AKT and MYC are two of the most prevalent oncogenes associated with prostate cancer. The precise effects of overexpression of these two key oncogenes on the regulation of metabolic pathways in prostate cancer are under active investigation; however, few studies have investigated their bivariate oncogene-pair expressions in metabolic prostate cancer phenotypes. This is primarily due to the lack of a suitable statistical method to analyze the data in the presence of oncogene interactions and within-metabolite-set correlations...
October 4, 2018: Computers in Biology and Medicine
Lisa N Barrow, Alan R Lemmon, Emily Moriarty Lemmon
Comparative phylogeography provides the necessary framework to examine the factors influencing population divergence, persistence, and change over time. Avise (2000) outlined four aspects of concordance that result when data exhibit significant phylogeographic signal: concordance among sites within a locus, among multiple loci within a species, among multiple species within a region, and between genetic patterns and established biogeographic provinces. To fully address each aspect of concordance, we combined target capture of a set of orthologous loci with targeted geographic sampling of multiple species, thus removing any variability introduced by using different genetic markers and heterogeneous sampling distributions...
November 1, 2018: Systematic Biology
Tetsuya Okuda
The data presented here pertain to a research article entitled "Structural characterization and dynamics of globotetraosylceramide in vascular endothelial cells under TNF-α stimulation" (Okuda et al., 2010). The present article provides additional structural and gene expression data for the characterization of a TNF-α-inducible glycosphingolipid, globotetraosylceramide (Gb4), in vascular endothelial cells. (i) Structural details of Gb4 in lipid raft-enriched cell membranes were determined by MALDI-TOF MS...
December 2018: Data in Brief
Saikou Y Bah, Thorsten Forster, Paul Dickinson, Beate Kampmann, Peter Ghazal
Background: Whole blood expression profiling is a mainstay for delineating differential diagnostic signatures of infection yet is subject to high variability that reduces power and complicates clinical usefulness. To date, confirmatory high confidence expression profiling signatures for clinical use remain uncertain. Here we have sought to evaluate the reproducibility and confirmatory nature of differential expression signatures, comprising molecular and cellular pathways, across multiple international clinical observational studies investigating children and adult whole blood transcriptome responses to tuberculosis (TB)...
2018: Frontiers in Genetics
Abdalla Elbialy, Shuichi Asakawa, Shugo Watabe, Shigeharu Kinoshita
Acromegaly is a pathological condition due to excess growth hormone (GH) secretion. Acromegaly patients exhibit a deterioration of health and many associated complications, such as cardiovascular issues, arthritis, kidney diseases, muscular weakness, and colon cancer. Since these complications are generalized throughout the body, we investigated the effect of GH excess on cellular integrity. Here, we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein (RFP) reporter gene for tracking GH gene expression throughout generations, and performed RNA-Seq data analysis from different organs...
October 17, 2018: Biology
Jianwei Lin, Yuchen Hou, Shanzhou Huang, Ziming Wang, Chengjun Sun, Zekang Wang, Xiaoshun He, Nga Lei Tam, Chenglin Wu, Linwei Wu
Exportin-T (XPOT) belongs to the RAN-GTPase exportin family that mediates export of tRNA from the nucleus to the cytoplasm. Up-regulation of XPOT indicates poor prognosis in breast cancer patients. However, the correlation between XPOT and hepatocellular carcinoma (HCC) remains unclear. Here, we found that high expression of XPOT in HCC indicated worse prognosis via bioinformatics analysis. Consistently, immunohistochemical staining of 95 pairs of tumors and adjacent normal liver tissues (ANLT) also showed up-regulation of XPOT...
October 18, 2018: Molecular Carcinogenesis
Saad Haider, Michael B Black, Bethany B Parks, Briana Foley, Barbara A Wetmore, Melvin E Andersen, Rebecca A Clewell, Kamel Mansouri, Patrick D McMullen
Efficient high-throughput transcriptomics (HTT) tools promise inexpensive, rapid assessment of possible biological consequences of human and environmental exposures to tens of thousands of chemicals in commerce. HTT systems have used relatively small sets of gene expression measurements coupled with mathematical prediction methods to estimate genome-wide gene expression and are often trained and validated using pharmaceutical compounds. It is unclear whether these training sets are suitable for general toxicity testing applications and the more diverse chemical space represented by commercial chemicals and environmental contaminants...
2018: Frontiers in Pharmacology
Tongwu Zhang, Jiyeon Choi, Michael A Kovacs, Jianxin Shi, Mai Xu, Alisa M Goldstein, Adam J Trower, D Timothy Bishop, Mark M Iles, David L Duffy, Stuart MacGregor, Laufey T Amundadottir, Matthew H Law, Stacie K Loftus, William J Pavan, Kevin M Brown
Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type-specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335 cis -eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05)...
October 17, 2018: Genome Research
Xiudong Guan, Lanxin Luo, Gulnaz Begum, Gary Kohanbash, Qingkun Song, Aparna Rao, Nduka Amankulor, Baoshan Sun, Dandan Sun, Wang Jia
BACKGROUND: Sodium/hydrogen exchanger 1 (NHE1), encoded by the SLC9A1 gene (SoLute Carrier family 9A1) in humans, is the main H+ efflux mechanism in maintaining alkaline intracellular pH (pHi ) and Warburg effects in glioma. However, to date, there are no clinical studies exploring pharmacological inhibition of NHE1 protein in cancer treatment. In this study, we investigated NHE1 expression in gliomas and its relationship with glioma clinical outcome. METHODS: The Chinese Glioma Genome Atlas (CGGA) dataset containing transcriptome sequencing data of 325 glioma samples and the Cancer Genome Atlas (TCGA) with 698 glioma mRNAseq data were analyzed in this study...
October 17, 2018: Journal of Experimental & Clinical Cancer Research: CR
Wen-Bin He, Wen-Juan Xiao, Yue-Qiu Tan, Xiao-Meng Zhao, Wen Li, Qian-Jun Zhang, Chang-Gao Zhong, Xiu-Rong Li, Liang Hu, Guang-Xiu Lu, Ge Lin, Juan Du
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD), the commonest inherited kidney disease, is generally caused by heterozygous mutations in PKD1, PKD2, or GANAB (PKD3). METHODS: We performed mutational analyses of PKD genes to identify causative mutations. A set of 90 unrelated families with ADPKD were subjected to mutational analyses of PKD genes. Genes were analysed using long-range PCR (LR-PCR), direct PCR sequencing, followed by multiplex ligation-dependent probe amplification (MLPA) or screening of GANAB for some patients...
October 17, 2018: BMC Medical Genetics
Paul Petrus, Niklas Mejhert, Patricia Corrales, Simon Lecoutre, Qian Li, Estela Maldonado, Agne Kulyté, Yamila Lopez, Mark Campbell, Juan R Acosta, Jurga Laurencikiene, Iyadh Douagi, Hui Gao, Concepción Martínez-Álvarez, Per Hedén, Kirsty L Spalding, Antonio Vidal-Puig, Gema Medina-Gomez, Peter Arner, Mikael Rydén
White adipose tissue (WAT) mass is determined by adipocyte size and number. While adipocytes are continuously turned over, the mechanisms controlling fat cell number in WAT upon weight changes are unclear. Herein, prospective studies of human subcutaneous WAT demonstrate that weight gain increases both adipocyte size and number, but the latter remains unaltered after weight loss. Transcriptome analyses associate changes in adipocyte number with the expression of 79 genes. This gene set is enriched for growth factors, out of which one, transforming growth factor-β3 (TGFβ3), stimulates adipocyte progenitor proliferation, resulting in a higher number of cells undergoing differentiation in vitro...
October 16, 2018: Cell Reports
Michael Tellier, Ronald Chalmers
Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. Here we show that the DNA-binding domain of the transposase targets the enzyme to transposon-end remnants and that this is capable of regulating gene expression, dependent on the methylase activity...
October 17, 2018: Nucleic Acids Research
Daniela Conrad, Sarah Wilker, Anna Schneider, Alexander Karabatsiakis, Anett Pfeiffer, Stephan Kolassa, Virginie Freytag, Vanja Vukojevic, Christian Vogler, Annette Milnik, Andreas Papassotiropoulos, Dominique J-F de Quervain, Thomas Elbert, Iris-Tatjana Kolassa
The risk of developing posttraumatic stress disorder (PTSD) increases with the number of traumatic event types experienced (trauma load) in interaction with other psychobiological risk factors. The NOTCH (neurogenic locus notch homolog proteins) signaling pathway, consisting of four different trans-membrane receptor proteins (NOTCH1-4), constitutes an evolutionarily well-conserved intercellular communication pathway (involved, e.g., in cell-cell interaction, inflammatory signaling, and learning processes). Its association with fear memory consolidation makes it an interesting candidate for PTSD research...
October 17, 2018: Psychophysiology
Sokratis A Apostolidis, Giuseppina Stifano, Tracy Tabib, Lisa M Rice, Christina M Morse, Bashar Kahaleh, Robert Lafyatis
Objective: The mechanisms that lead to endothelial cell (EC) injury and propagate the vasculopathy in Systemic Sclerosis (SSc) are not well understood. Using single cell RNA sequencing (scRNA-seq), our goal was to identify EC markers and signature pathways associated with vascular injury in SSc skin. Methods: We implemented single cell sorting and subsequent RNA sequencing of cells isolated from SSc and healthy control skin. We used t-distributed stochastic neighbor embedding (t-SNE) to identify the various cell types...
2018: Frontiers in Immunology
Takahiro Kodama, Jing Yi, Justin Y Newberg, Jean C Tien, Hao Wu, Milton J Finegold, Michiko Kodama, Zhubo Wei, Takeshi Tamura, Tetsuo Takehara, Randy L Johnson, Nancy A Jenkins, Neal G Copeland
Nonalcoholic fatty liver disease (NAFLD) is the fastest rising cause of hepatocellular carcinoma (HCC) in Western countries; however, the molecular mechanisms that cause NAFLD-HCC remain elusive. To identify molecular drivers of NAFLD-HCC, we performed Sleeping Beauty (SB) transposon mutagenesis screens in liver-specific Pten knockout and in high-fat diet-fed mice, which are murine models of NAFLD-HCC. SB mutagenesis accelerated liver tumor formation in both models and identified 588 and 376 candidate cancer genes (CCGs), respectively; 257 CCGs were common to both screens and were enriched in signaling pathways known to be important for human HCC...
October 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
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