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Jiang J, Wang C, Qi R, Fu H, Ma Q. scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease. iScience 2020; 23:101769. [PMID: 33241205 PMCID: PMC7674513 DOI: 10.1016/j.isci.2020.101769] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder of the brain and the most common form of dementia among the elderly. The single-cell RNA-sequencing (scRNA-Seq) and single-nucleus RNA-sequencing (snRNA-Seq) techniques are extremely useful for dissecting the function/dysfunction of highly heterogeneous cells in the brain at the single-cell level, and the corresponding data analyses can significantly improve our understanding of why particular cells are vulnerable in AD. We developed an integrated database named scREAD (single-cell RNA-Seq database for Alzheimer's disease), which is as far as we know the first database dedicated to the management of all the existing scRNA-Seq and snRNA-Seq data sets from the human postmortem brain tissue with AD and mouse models with AD pathology. scREAD provides comprehensive analysis results for 73 data sets from 10 brain regions, including control atlas construction, cell-type prediction, identification of differentially expressed genes, and identification of cell-type-specific regulons.
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Affiliation(s)
- Jing Jiang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Cankun Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Ren Qi
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Hongjun Fu
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
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Martin R, Löchel HF, Welzel M, Hattab G, Hauschild AC, Heider D. CORDITE: The Curated CORona Drug InTERactions Database for SARS-CoV-2. iScience 2020; 23:101297. [PMID: 32619700 PMCID: PMC7305714 DOI: 10.1016/j.isci.2020.101297] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 01/18/2023] Open
Abstract
Since the outbreak in 2019, researchers are trying to find effective drugs against the SARS-CoV-2 virus based on de novo drug design and drug repurposing. The former approach is very time consuming and needs extensive testing in humans, whereas drug repurposing is more promising, as the drugs have already been tested for side effects, etc. At present, there is no treatment for COVID-19 that is clinically effective, but there is a huge amount of data from studies that analyze potential drugs. We developed CORDITE to efficiently combine state-of-the-art knowledge on potential drugs and make it accessible to scientists and clinicians. The web interface also provides access to an easy-to-use API that allows a wide use for other software and applications, e.g., for meta-analysis, design of new clinical studies, or simple literature search. CORDITE is currently empowering many scientists across all continents and accelerates research in the knowledge domains of virology and drug design.
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Affiliation(s)
- Roman Martin
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
| | - Hannah F Löchel
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
| | - Marius Welzel
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
| | - Anne-Christin Hauschild
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-University of Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany.
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Churchill CDM, Winter P, Tuszynski JA, Levin M. EDEn-Electroceutical Design Environment: Ion Channel Tissue Expression Database with Small Molecule Modulators. iScience 2019; 11:42-56. [PMID: 30590250 PMCID: PMC6308252 DOI: 10.1016/j.isci.2018.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/22/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The emerging field of bioelectricity has revealed numerous new roles for ion channels beyond the nervous system, which can be exploited for applications in regenerative medicine. Developing such biomedical interventions for birth defects, cancer, traumatic injury, and bioengineering first requires knowledge of ion channel targets expressed in tissues of interest. This information can then be used to select combinations of small molecule inhibitors and/or activators that manipulate the bioelectric state. Here, we provide an overview of electroceutical design environment (EDEn), the first bioinformatic platform that facilitates the design of such therapeutic strategies. This database includes information on ion channels and ion pumps, linked to known chemical modulators and their properties. The database also provides information about the expression levels of the ion channels in over 100 tissue types. The graphical interface allows the user to readily identify chemical entities that can alter the electrical properties of target cells and tissues.
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Affiliation(s)
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Michael Levin
- Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
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Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience 2018; 10:247-264. [PMID: 30553813 PMCID: PMC6302245 DOI: 10.1016/j.isci.2018.11.029] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/11/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022] Open
Abstract
CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, NCI-SCLC, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics and gene regulatory network analyses, and exploration of pharmacogenomic determinants and drug signatures. It leverages overlaps of cell lines and drugs across databases to examine reproducibility and expand pathway analyses. We illustrate the value of CellMinerCDB for elucidating gene expression determinants, such as DNA methylation and copy number variations, and highlight complexities in assessing mutational burden. We demonstrate the value of CellMinerCDB in selecting drugs with reproducible activity, expand on the dominant role of SLFN11 for drug response, and present novel response determinants and genomic signatures for topoisomerase inhibitors and schweinfurthins. We also introduce LIX1L as a gene associated with mesenchymal signature and regulation of cellular migration and invasiveness.
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Affiliation(s)
- Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA.
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Lisa Loman
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Margot Sunshine
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Francesco Iorio
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Fabricio G Sousa
- Centro De Estudos Em Células Tronco, Terapia Celular E Genética Toxicológica, Programa De Pós-Graduação Em Farmácia, Universidade Federal De Mato Grosso Do Sul, Campo Grande, MS 79070-900, Brazil
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Kurt W Kohn
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mathew Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Abstract
Beyond its direct involvement in protein synthesis with mRNA, tRNA, and rRNA, RNA is now being appreciated for its significance in the overall metabolism and regulation of the cell. Comparative analysis has been very effective in the identification and characterization of RNA molecules, including the accurate prediction of their secondary structure. We are developing an integrative scalable data management and analysis system, the RNA Comparative Analysis Database (rCAD), implemented with SQL Server to support RNA comparative analysis. The platformagnostic database schema of rCAD captures the essential relationships between the different dimensions of information for RNA comparative analysis datasets. The rCAD implementation enables a variety of comparative analysis manipulations with multiple integrated data dimensions for advanced RNA comparative analysis workflows. In this paper, we describe details of the rCAD schema design and illustrate its usefulness with two usage scenarios.
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