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SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete.
BACKGROUND: Sox proteins encompass an evolutionarily conserved family of transcription factors with critical roles in animal development and stem cell biology. In common with vertebrates, the Drosophila group B proteins SoxNeuro...
Distinctive regulatory architectures of germline-active and somatic genes in C. elegans.
Jacques Serizay, Yan Dong, Jürgen Jänes, Michael Chesney, Chiara Cerrato, Julie Ahringer
Jan 18, 2021
RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared...
Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.
Adrienne Tin, Jonathan Marten, Victoria L Halperin Kuhns, Yong Li, Matthias Wuttke, Holger Kirsten, Karsten B Sieber, Chengxiang Qiu, Mathias Gorski, Zhi Yu, Ayush Giri, Gardar Sveinbjornsson, Man Li, Audrey Y Chu, Anselm Hoppmann, Luke J O'Connor, Bram Prins, Teresa Nutile, Damia Noce, Masato Akiyama, Massimiliano Cocca, Sahar Ghasemi, Peter J van der Most, Katrin Horn, Yizhe Xu, Christian Fuchsberger, Sanaz Sedaghat, Saima Afaq, Najaf Amin, Johan Ärnlöv, Stephan JL Bakker, Nisha Bansal, Daniela Baptista, Sven Bergmann, Mary L Biggs, Ginevra Biino, Eric Boerwinkle, Erwin P Bottinger, Thibaud S Boutin, Marco Brumat, Ralph Burkhardt, Eric Campana, Archie Campbell, Harry Campbell, Robert J Carroll, Eulalia Catamo, John C Chambers, Marina Ciullo, Maria Pina Concas, Josef Coresh, Tanguy Corre, Daniele Cusi, Sala Cinzia Felicita, Martin H de Borst, Alessandro De Grandi, Renée de Mutsert, Aiko PJ de Vries, Graciela Delgado, Ayşe Demirkan, Olivier Devuyst, Katalin Dittrich, Kai-Uwe Eckardt, Georg Ehret, Karlhans Endlich, Michele K Evans, Ron T Gansevoort, Paolo Gasparini, Vilmantas Giedraitis, Christian Gieger, Giorgia Girotto, Martin Gögele, Scott D Gordon, Daniel F Gudbjartsson, Vilmundur Gudnason, German Chronic Kidney Disease Study, Toomas Haller, Pavel Hamet, Tamara B Harris, Caroline Hayward, Andrew A Hicks, Edith Hofer, Hilma Holm, Wei Huang, Nina Hutri-Kähönen, Shih-Jen Hwang, M Arfan Ikram, Raychel M Lewis, Erik Ingelsson, Johanna Jakobsdottir, Ingileif Jonsdottir, Helgi Jonsson, Peter K Joshi, Navya Shilpa Josyula, Bettina Jung, Mika Kähönen, Yoichiro Kamatani, Masahiro Kanai, Shona M Kerr, Wieland Kiess, Marcus E Kleber, Wolfgang Koenig, Jaspal S Kooner, Antje Körner, Peter Kovacs, Bernhard K Krämer, Florian Kronenberg, Michiaki Kubo, Brigitte Kühnel, Martina La Bianca, Leslie A Lange, Benjamin Lehne, Terho Lehtimäki, Lifelines Cohort Study, Jun Liu, Markus Loeffler, Ruth JF Loos, Leo-Pekka Lyytikäinen, Reedik Magi, Anubha Mahajan, Nicholas G Martin, Winfried März, Deborah Mascalzoni, Koichi Matsuda, Christa Meisinger, Thomas Meitinger, Andres Metspalu, Yuri Milaneschi, V. A. Million Veteran Program, Christopher J O'Donnell, Otis D Wilson, J Michael Gaziano, Pashupati P Mishra, Karen L Mohlke, Nina Mononen, Grant W Montgomery, Dennis O Mook-Kanamori, Martina Müller-Nurasyid, Girish N Nadkarni, Mike A Nalls, Matthias Nauck, Kjell Nikus, Boting Ning, Ilja M Nolte, Raymond Noordam, Jeffrey R O'Connell, Isleifur Olafsson, Sandosh Padmanabhan, Brenda WJH Penninx, Thomas Perls, Annette Peters, Mario Pirastu, Nicola Pirastu, Giorgio Pistis, Ozren Polasek, Belen Ponte, David J Porteous, Tanja Poulain, Michael H Preuss, Ton J Rabelink, Laura M Raffield, Olli T Raitakari, Rainer Rettig, Myriam Rheinberger, Kenneth M Rice, Federica Rizzi, Antonietta Robino, Igor Rudan, Alena Krajcoviechova, Renata Cifkova, Rico Rueedi, Daniela Ruggiero, Kathleen A Ryan, Yasaman Saba, Erika Salvi, Helena Schmidt, Reinhold Schmidt, Christian M Shaffer, Albert V Smith, Blair H Smith, Cassandra N Spracklen, Konstantin Strauch, Michael Stumvoll, Patrick Sulem, Salman M Tajuddin, Andrej Teren, Joachim Thiery, Chris HL Thio, Unnur Thorsteinsdottir, Daniela Toniolo, Anke Tönjes, Johanne Tremblay, André G Uitterlinden, Simona Vaccargiu, Pim van der Harst, Cornelia M van Duijn, Niek Verweij, Uwe Völker, Peter Vollenweider, Gerard Waeber, Melanie Waldenberger, John B Whitfield, Sarah H Wild, James F Wilson, Qiong Yang, Weihua Zhang, Alan B Zonderman, Murielle Bochud, James G Wilson, Sarah A Pendergrass, Kevin Ho, Afshin Parsa, Peter P Pramstaller, Bruce M Psaty, Carsten A Böger, Harold Snieder, Adam S Butterworth, Yukinori Okada, Todd L Edwards, Kari Stefansson, Katalin Susztak, Markus Scholz, Iris M Heid, Adriana M Hung, Alexander Teumer, Cristian Pattaro, Owen M Woodward, Veronique Vitart, Anna Köttgen
Oct 17, 2019
ATP Binding Cassette Transporter Subfamily G Member 2 Cardiovascular Diseases Cohort Studies Genetic Loci Genetic Markers Genetic Predisposition to Disease Genome-Wide Association Study gout Hepatocyte Nuclear Factor 1-alpha Hepatocyte Nuclear Factor 4 Humans Kidney Liver Metabolic Diseases Neoplasm Proteins Organ Specificity Polymorphism Single Nucleotide Signal Transduction Uric Acid
Common genetic variation drives molecular heterogeneity in human iPSCs.
Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver J Culley, Petr Danecek, Adam Faulconbridge, Peter W Harrison, Annie Kathuria, Davis McCarthy, Shane A McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Alice Mann, Ian Streeter, Chukwuma A Agu, Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Alistair White, Sharad R Patel, Laura Clarke, Reena Halai, Christopher M Kirton, Anja Kolb-Kokocinski, Philip Beales, Ewan Birney, Davide Danovi, Angus I Lamond, Willem H Ouwehand, Ludovic Vallier, Fiona M Watt, Richard Durbin, Oliver Stegle, Daniel J Gaffney
Nov 20, 2018
Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS...
Brain glucose sensing, glucokinase and neural control of metabolism and islet function.
glucokinase glucose sensing glucose-stimulated insulin secretion hypoglycaemia Hypothalamus Insulin Animals Brain Diabetes mellitus Energy Metabolism Feedback Physiological Glucokinase Glucose Humans Hypoglycemia Insulin Insulin Secretion Islets of Langerhans Models Neurological Nerve Tissue Proteins Neuroglia Neurons obesity Organ Specificity
Cross-tissue immune cell analysis reveals tissue-specific features in humans.
C Domínguez Conde, C Xu, LB Jarvis, DB Rainbow, SB Wells, T Gomes, SK Howlett, O Suchanek, K Polanski, HW King, L Mamanova, N Huang, PA Szabo, L Richardson, L Bolt, ES Fasouli, KT Mahbubani, M Prete, L Tuck, N Richoz, ZK Tuong, L Campos, HS Mousa, EJ Needham, S Pritchard, T Li, R Elmentaite, J Park, E Rahmani, D Chen, DK Menon, OA Bayraktar, LK James, KB Meyer, N Yosef, MR Clatworthy, PA Sims, DL Farber, K Saeb-Parsy, JL Jones, SA Teichmann
Jun 13, 2022
Leukemia-associated Rho guanine-nucleotide exchange factor is not critical for RhoA regulation, yet is important for platelet activation and thrombosis in mice.
BACKGROUND: RhoA is an important regulator of platelet responses downstream of Gα13 , yet we still know little about its regulation in platelets. Leukemia-associated Rho guanine-nucleotide exchange factor (GEF [LARG]), a RhoA...
Larg protein mouse RhoA protein mouse gene knockout MOUSE platelets Thrombosis 15-Hydroxy-11 alpha 9 alpha-(epoxymethano)prosta-5 13-dienoic Acid Adenosine Diphosphate Animals Blood Platelets Cell Degranulation Chlorides Crosses Genetic Ferric Compounds Gene Knockout Techniques Mice Mice Knockout Oligopeptides Organ Specificity Platelet Activation Platelet Aggregation Rho Guanine Nucleotide Exchange Factors Thrombosis rho GTP-Binding Proteins rhoA GTP-Binding Protein
Group 2 innate lymphocytes at the interface between innate and adaptive immunity.
Group 2 innate lymphoid cells (ILC2) are innate immune cells that respond rapidly to their environment through soluble inflammatory mediators and cell-to-cell interactions. As tissue-resident sentinels, ILC2 help orchestrate...
ILC2 T helper cells TH2 innate lymphoid cells type 2 response Adaptive Immunity Animals Cell Differentiation Cytokines Hormones Humans Immunity Innate Interleukins Lipids Lymphocyte Activation Lymphocyte Subsets Mice Models Immunological Neuroimmunomodulation Organ Specificity Receptors Immunologic Thymic Stromal Lymphopoietin
Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation.
Clara Y Cheong, Keefe Chng, Shilen Ng, Siew Boom Chew, Louiza Chan, Anne C Ferguson-Smith
Jun 11, 2015
Animals Base Sequence DNA Methylation DNA-Binding Proteins Female Genomic Imprinting Humans Inositol Polyphosphate 5-Phosphatases Kruppel-Like Transcription Factors Macaca fascicularis Male Mice Molecular Sequence Data Oocytes Organ Specificity Phosphoric Monoester Hydrolases RNA Long Noncoding Species Specificity
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae.
Dean A Baker, Tony Nolan, Bettina Fischer, Alex Pinder, Andrea Crisanti, Steven Russell
Jul 05, 2011
Insulin-like Growth Factor II
Amber N Ziegler, Qiang Feng, Shravanthi Chidambaram, Jaimie M Testai, Ekta Kumari, Deborah E Rothbard, Miguel Constancia, Ionel Sandovici, Tara Cominski, Kevin Pang, Nan Gao, Teresa L Wood, Steven W Levison
Apr 05, 2019
Tissue-specific stem cells have unique properties and growth requirements, but a small set of juxtacrine and paracrine signals have been identified that are required across multiple niches. Whereas insulin-like growth factor II...
IGF-II crypt of Lieberkühn intestinal stem cell neural stem cell Neurogenesis subgranular zone subventricular zone Adult stem cells Animals Biomarkers Brain Cell Differentiation Immunohistochemistry Insulin-Like Growth Factor II Intestines Mice Mice Knockout Mice Transgenic Neurogenesis Olfactory Bulb Organ Specificity Stem Cell Niche
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation.
Arianne C Richard, Paul A Lyons, James E Peters, Daniele Biasci, Shaun M Flint, James C Lee, Eoin F McKinney, Richard M Siegel, Kenneth GC Smith
Sep 24, 2018
BACKGROUND: Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of...
MT-HESS
Alex Lewin, Habib Saadi, James E Peters, Aida Moreno-Moral, James C Lee, Kenneth GC Smith, Enrico Petretto, Leonardo Bottolo, Sylvia Richardson
Sep 05, 2018
MOTIVATION: Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of...
Algorithms Animals Bayes Theorem Diabetes mellitus Type 1 Gene Expression Regulation Gene Regulatory Networks Genomics Humans Inflammation Inflammatory Bowel Diseases Models Theoretical Organ Specificity Polymorphism Single Nucleotide Programming Languages Quantitative Trait Loci Rats Software Tissue Distribution
Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development.
Fabienne Lescroart, Samira Chabab, Xionghui Lin, Steffen Rulands, Catherine Paulissen, Annie Rodolosse, Herbert Auer, Younes Achouri, Christine Dubois, Antoine Bondue, Benjamin D Simons, Cédric Blanpain
Sep 30, 2014
The fragilis interferon-inducible gene family of transmembrane proteins is associated with germ cell specification in mice.
BACKGROUND: Specification of primordial germ cells in mice depends on instructive signalling events, which act first to confer germ cell competence on epiblast cells, and second, to impose a germ cell fate upon competent...
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.
Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T Odom, Paul Flicek
Feb 18, 2021
Enhancers Gene regulation LINE L1 LINE L2 Long Interspersed Nuclear Elements (LINEs) Mammals Promoters regulatory evolution transposable elements Animals Chromosome Mapping Conserved Sequence Enhancer Elements Genetic evolution Molecular Gene Expression Regulation Humans Long Interspersed Nucleotide Elements Mammals Organ Specificity Promoter Regions Genetic Regulatory Sequences Nucleic Acid Retroelements
The activating mutation R201C in GNAS promotes intestinal tumourigenesis in Apc(Min/+) mice through activation of Wnt and ERK1/2 MAPK pathways.
Somatically acquired, activating mutations of GNAS, the gene encoding the stimulatory G-protein Gsalpha subunit, have been identified in kidney, thyroid, pituitary, leydig cell, adrenocortical and, more recently, in colorectal...
Adenoma Adenomatous Polyposis Coli Protein Alleles Animals Cell Differentiation Cell Proliferation Chromogranins Colorectal Neoplasms Cyclic AMP Disease Progression Epithelial Cells Female GTP-Binding Protein alpha Subunits Gs Gene Expression Regulation Neoplastic Genetic Loci Humans Intestinal Mucosa MAP Kinase Signaling System Male Membrane Glycoproteins Mice Mitogen-Activated Protein Kinase 1 Mitogen-Activated Protein Kinase 3 Mutant Proteins Mutation Organ Specificity Phosphoric Diester Hydrolases Promoter Regions Genetic Stem Cells Substrate Specificity Up-Regulation Wnt Proteins
p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response.
Hiroyoshi Hattori, Rekin's Janky, Wilfried Nietfeld, Stein Aerts, M Madan Babu, Ashok R Venkitaraman
Feb 13, 2020
The human DNA damage response (DDR) triggers profound changes in gene expression, whose nature and regulation remain uncertain. Although certain micro-(mi)RNA species including miR34, miR-18, miR-16 and miR-143 have been...
AP-1 activator protein-1 DDR DNA damage response DNA damage response E2F1 transcription factor E2F1 FOXM1 forkhead box protein M1 NF-k B nuclear factor-k B NGS next-generation sequencing TF transcription factor TP53 tumour protein p53 clinical outcome computational analysis double stranded DNA breaks DSBs ionizing radiation IR miRNA micro-RNA micro-RNA misc RNA miscellaneous RNA next-generation sequencing p53 scRNA small cytoplasmic RNA snRNA small nuclear RNA snoRNA small nucleolar RNA tRNA transfer RNA Cell Line DNA Damage DNA Repair Gene Expression Regulation Gene Expression Regulation Neoplastic Genome Genome Human Humans MicroRNAs Neoplasms Organ Specificity Tumor Suppressor Protein p53
Transcript analysis reveals a specific HOX signature associated with positional identity of human endothelial cells.
Mark Toshner, Benjamin J Dunmore, Eoin F McKinney, Mark Southwood, Paola Caruso, Paul D Upton, John P Waters, Mark L Ormiston, Jeremy N Skepper, Gerard Nash, Amer A Rana, Nicholas W Morrell
Jun 14, 2018
The endothelial cell has a remarkable ability for sub-specialisation, adapted to the needs of a variety of vascular beds. The role of developmental programming versus the tissue contextual environment for this specialization is...
Adult Animals Cell Differentiation Cell Line Cluster Analysis Embryonic Stem Cells Endothelial Cells Fetus Gene Expression Profiling Gene Ontology Genes Homeobox Homeodomain Proteins Humans Lung Mice Neovascularization Physiologic Oligonucleotide Array Sequence Analysis Organ Specificity Phenotype Pulmonary Artery RNA Messenger Rats Real-Time Polymerase Chain Reaction Reproducibility of Results
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits.
Here, we performed a comprehensive intra-tissue and inter-tissue multilayer network analysis of the human transcriptome. We generated an atlas of communities in gene co-expression networks in 49 tissues (GTEx v8), evaluated...
Mapping the developing human immune system across organs.
Chenqu Suo, Emma Dann, Issac Goh, Laura Jardine, Vitalii Kleshchevnikov, Jong-Eun Park, Rachel A Botting, Emily Stephenson, Justin Engelbert, Zewen Kelvin Tuong, Krzysztof Polanski, Nadav Yayon, Chuan Xu, Ondrej Suchanek, Rasa Elmentaite, Cecilia Domínguez Conde, Peng He, Sophie Pritchard, Mohi Miah, Corina Moldovan, Alexander S Steemers, Pavel Mazin, Martin Prete, Dave Horsfall, John C Marioni, Menna R Clatworthy, Muzlifah Haniffa, Sarah A Teichmann
Jun 13, 2022
Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing the developing immune system as a distributed network across tissues. We profiled nine...
Expression Atlas update
Irene Papatheodorou, Pablo Moreno, Jonathan Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F Jarnuczak, Simon Jupp, John Marioni, Kerstin Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah Teichmann, Juan Antonio Vizcaino, Alvis Brazma
Dec 19, 2019
Expression Atlas is EMBL-EBI's resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to...
Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants.
Elodie Persyn, Ken B Hanscombe, Joanna MM Howson, Cathryn M Lewis, Matthew Traylor, Hugh S Markus
Mar 30, 2020
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