A gene atlas of the mouse and human protein-encoding transcriptomes.
- Authors
- Su, Andrew I; Wiltshire, Tim; Batalov, Serge; Lapp, Hilmar; Ching, Keith A; Block, David; Zhang, Jie; Soden, Richard; Hayakawa, Mimi; Kreiman, Gabriel; Cooke, Michael P; Walker, John R; Hogenesch, John B
- Year
- 2004
- Journal
- Proceedings of the National Academy of Sciences of the United States of America
- PMID
- 15075390
- DOI
- 10.1073/pnas.0400782101
- PMCID
- PMC395923
The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting.
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| Melanoma Cell Intrinsic GABA<sub>A</sub> Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity. | Pomeranz Krummel DA et al. | β | 2021 | β |
| Molecular Analysis of <i>14-3-3</i> Genes in <i>Citrus sinensis</i> and Their Responses to Different Stresses. | Lyu S et al. | β | 2021 | β |
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| Weighted Gene Co-Expression Network Analysis Identifies ANGPTL4 as a Key Regulator in Diabetic Cardiomyopathy <i>via</i> FAK/SIRT3/ROS Pathway in Cardiomyocyte. | Dai L et al. | β | 2021 | β |
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| Evaluation of the Performance of Lipidyzer Platform and Its Application in the Lipidomics Analysis in Mouse Heart and Liver. | Cao Z et al. | β | 2020 | β |
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| Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. | Thompson AJ et al. | β | 2020 | β |
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| Placenta-Specific Genes, Their Regulation During Villous Trophoblast Differentiation and Dysregulation in Preterm Preeclampsia. | Szilagyi A et al. | β | 2020 | β |
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| Recent advances in blood pressure research. | Mrowka R | β | 2020 | β |
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| The transcription factor C/EBPΞ² orchestrates dendritic cell maturation and functionality under homeostatic and malignant conditions. | Scholz F et al. | β | 2020 | β |
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| An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer. | Leung SW et al. | β | 2019 | β |
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| CD73 expression in normal and pathological human hepatobiliopancreatic tissues. | Sciarra A et al. | β | 2019 | β |
| Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq. | Feng X et al. | β | 2019 | β |
| Characterization of mRNA profiles of the exosome-like vesicles in porcine follicular fluid. | Matsuno Y et al. | β | 2019 | β |
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| Consequences of the Endogenous N-Glycosylation of Human Ribonuclease 1. | Ressler VT et al. | β | 2019 | β |
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| Deletion of Adam6 in Mus musculus leads to male subfertility and deficits in sperm ascent into the oviduct. | Voronina VA et al. | β | 2019 | β |
| DENND5B Regulates Intestinal Triglyceride Absorption and Body Mass. | Gordon SM et al. | β | 2019 | β |
| Differences in Gene Expression in Older Compared With Younger Kidney Transplant Recipients. | Schaenman JM et al. | β | 2019 | β |
| Disruption of the Sensory System Affects Sterile Cutaneous Inflammation InΒ Vivo. | La Russa F et al. | β | 2019 | β |
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| Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8<sup>+</sup> Dendritic Cells. | Zwick M et al. | β | 2019 | β |
| Falling in love is associated with immune system gene regulation. | Murray DR et al. | β | 2019 | β |
| Fighting rheumatoid arthritis: Kv1.3 as a therapeutic target. | Serrano-AlbarrΓ‘s A et al. | β | 2019 | β |
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| Functional rare and low frequency variants in BLK and BANK1 contribute to human lupus. | Jiang SH et al. | β | 2019 | β |
| Gas6/TAM System: A Key Modulator of the Interplay between Inflammation and Fibrosis. | Bellan M et al. | β | 2019 | β |
| Genetic Influences on the Amount of Cell Death in the Neural Tube of BXD Mice Exposed to Acute Ethanol at Midgestation. | ThΓ©berge ET et al. | β | 2019 | β |
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| Hsp70 Binds to the Androgen Receptor N-terminal Domain and Modulates the Receptor Function in Prostate Cancer Cells. | Dong J et al. | β | 2019 | β |
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| Insights into the Signal Transduction Pathways of Mouse Lung Type II Cells Revealed by Transcription Factor Profiling in the Transcriptome. | Ramana CV | β | 2019 | β |
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| Molecular characterization and expression regulation of the factor-inhibiting HIF-1 (FIH-1) gene under hypoxic stress in bighead carp (Aristichthys nobilis). | Feng X et al. | β | 2019 | β |
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| Mouse screen reveals multiple new genes underlying mouse and human hearing loss. | Ingham NJ et al. | β | 2019 | β |
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| Novel Genetic Locus Influencing Retinal Venular Tortuosity Is Also Associated With Risk of Coronary Artery Disease. | Veluchamy A et al. | β | 2019 | β |
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| Quantifying Gene Essentiality Based on the Context of Cellular Components. | Jia K et al. | β | 2019 | β |
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| The Absence of NOD1 Enhances Killing of <i>Aspergillus fumigatus</i> Through Modulation of Dectin-1 Expression. | Gresnigt MS et al. | β | 2017 | β |
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| The Emerging Role of MORC Family Proteins in Cancer Development and Bone Homeostasis. | Hong G et al. | β | 2017 | β |
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| The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated with F508del CFTR Mutations. | Agrawal PB et al. | β | 2017 | β |
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| Moving from capstones toward cornerstones: successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders. | Kopp N et al. | β | 2015 | β |
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| Pedican: an online gene resource for pediatric cancers with literature evidence. | Zhao M et al. | β | 2015 | β |
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| Potential mechanisms to explain how LABAs and PDE4 inhibitors enhance the clinical efficacy of glucocorticoids in inflammatory lung diseases. | Giembycz MA et al. | β | 2015 | β |
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| Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. | Nestor CE et al. | β | 2015 | β |
| Reduced Penetrance of PRRT2 Mutation in a Chinese Family With Infantile Convulsion and Choreoathetosis Syndrome. | Zhang LM et al. | β | 2015 | β |
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| Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. | Mohammadi S et al. | β | 2015 | β |
| Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. | TaΕan M et al. | β | 2015 | β |
| Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. | Dunyak BM et al. | β | 2015 | β |
| Single-Nucleotide Polymorphisms in Pig EPHX1 Gene are Associated with Pork Quality Traits. | Cho HR et al. | β | 2015 | β |
| SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm. | Hamblett KJ et al. | β | 2015 | β |
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| Spatial and temporal expression of immunoglobulin superfamily member 1 in the rat. | Joustra SD et al. | β | 2015 | β |
| SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. | Micale G et al. | β | 2015 | β |
| Stem Cell Differentiation Stage Factors from Zebrafish Embryo: A Novel Strategy to Modulate the Fate of Normal and Pathological Human (Stem) Cells. | Biava PM et al. | β | 2015 | β |
| Susceptibility variants in the CD58 gene locus point to a role of microRNA-548ac in the pathogenesis of multiple sclerosis. | Hecker M et al. | β | 2015 | β |
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| Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation. | Pandya S et al. | β | 2015 | β |
| The basic helix-loop-helix transcription factor E47 reprograms human pancreatic cancer cells to a quiescent acinar state with reduced tumorigenic potential. | Kim S et al. | β | 2015 | β |
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| Profiling the transcription factor regulatory networks of human cell types. | Zhang S et al. | β | 2014 | β |
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| Role of synucleins in traumatic brain injury β an experimental in vitro and in vivo study in mice. | Surgucheva I et al. | β | 2014 | β |
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| Tespa1 negatively regulates FcΞ΅RI-mediated signaling and the mast cell-mediated allergic response. | Wang D et al. | β | 2014 | β |
| The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. | Peng X et al. | β | 2014 | β |
| The GTPase-activating protein GIT2 protects against colitis by negatively regulating Toll-like receptor signaling. | Wei J et al. | β | 2014 | β |
| The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling. | Lindskog C et al. | β | 2014 | β |
| The mammalian Doublesex homolog DMRT6 coordinates the transition between mitotic and meiotic developmental programs during spermatogenesis. | Zhang T et al. | β | 2014 | β |
| The role of H3K4me3 and H3K9/14ac in the induction by dexamethasone of Per1 and Sgk1, two glucocorticoid [corrected] early response genes that mediate the effects of acute stress in mammals. | Xydous M et al. | β | 2014 | β |
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| The transcriptomic and proteomic landscapes of bone marrow and secondary lymphoid tissues. | Andersson S et al. | β | 2014 | β |
| Transcription factors involved in prostate gland adaptation to androgen deprivation. | Rosa-Ribeiro R et al. | β | 2014 | β |
| Transcriptomic analysis of mononuclear phagocyte differentiation and activation. | Hume DA et al. | β | 2014 | β |
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| Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. | Dimitrieva S et al. | β | 2014 | β |
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