Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes
| Autor: | Leopold M.G. Curfs, Chris T. Evelo, Friederike Ehrhart, Susan L. Coort, Eric Smeets, Elisa Cirillo, Nasim Bahram Sangani, Lars M. T. Eijssen |
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| Přispěvatelé: | Bioinformatica, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, RS: FHML MaCSBio |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
EXPRESSION
congenital hereditary and neonatal diseases and abnormalities Cytoskeleton organization Methyl-CpG-Binding Protein 2 Rett syndrome Context (language use) Computational biology Biology medicine.disease_cause MECP2 LINKS Transcriptome 03 medical and health sciences 0302 clinical medicine Gene expression medicine Humans neurological disorder BRAIN CYTOSCAPE DLX5 Gene MUTATION Biological Psychiatry METAANALYSIS Mutation REPRESSION rare diseases bioinformatics medicine.disease Phenotype 030227 psychiatry pathway analysis Psychiatry and Mental health GROWTH |
| Zdroj: | World Journal of Biological Psychiatry, 21(10), 712-725. Routledge/Taylor & Francis Group |
| ISSN: | 1814-1412 1562-2975 |
| Popis: | Rett syndrome (RTT) is a rare disorder causing severe intellectual and physical disability. The cause is a mutation in the gene coding for the methyl-CpG binding protein 2 (MECP2), a multifunctional regulator protein. Purpose of the study was integration and investigation of multiple gene expression profiles in human cells with impaired MECP2 gene to obtain a data-driven insight in downstream effects. Information about changed gene expression was extracted from five previously published studies. We identified a set of genes which are significantly changed not in all but several transcriptomics datasets and were not mentioned in the context of RTT before. Using overrepresentation analysis of molecular pathways and gene ontology we found that these genes are involved in several processes and molecular pathways known to be affected in RTT. Integrating transcription factors we identified a possible link how MECP2 regulates cytoskeleton organization via MEF2C and CAPG. Integrative analysis of omics data and prior knowledge databases is a powerful approach to identify links between mutation and phenotype especially in rare disease research where little data is available.AbbreviationsRett syndrome (RTT), embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), fold change (FC), Gene Ontology (GO), EIF (eukaryotic initiation of transcription factor)For genes the symbols according to the HGNC nomenclature were used. |
| Databáze: | OpenAIRE |
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