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Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome

In this study, biomarkers and transcriptional factor motifs were identified in order to investigate the etiology and phenotypic severity of Down syndrome. GSE 1281, GSE 1611, and GSE 5390 were downloaded from the gene expression ominibus (GEO). A robust multiarray analysis (RMA) algorithm was applie...

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Autores principales: Kong, X.D., Liu, N., Xu, X.J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Associação Brasileira de Divulgação Científica 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181218/
https://www.ncbi.nlm.nih.gov/pubmed/25118625
http://dx.doi.org/10.1590/1414-431X20143792
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author Kong, X.D.
Liu, N.
Xu, X.J.
author_facet Kong, X.D.
Liu, N.
Xu, X.J.
author_sort Kong, X.D.
collection PubMed
description In this study, biomarkers and transcriptional factor motifs were identified in order to investigate the etiology and phenotypic severity of Down syndrome. GSE 1281, GSE 1611, and GSE 5390 were downloaded from the gene expression ominibus (GEO). A robust multiarray analysis (RMA) algorithm was applied to detect differentially expressed genes (DEGs). In order to screen for biological pathways and to interrogate the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, the database for annotation, visualization, and integrated discovery (DAVID) was used to carry out a gene ontology (GO) function enrichment for DEGs. Finally, a transcriptional regulatory network was constructed, and a hypergeometric distribution test was applied to select for significantly enriched transcriptional factor motifs. CBR1, DYRK1A, HMGN1, ITSN1, RCAN1, SON, TMEM50B, and TTC3 were each up-regulated two-fold in Down syndrome samples compared to normal samples; of these, SON and TTC3 were newly reported. CBR1, DYRK1A, HMGN1, ITSN1, RCAN1, SON, TMEM50B, and TTC3 were located on human chromosome 21 (mouse chromosome 16). The DEGs were significantly enriched in macromolecular complex subunit organization and focal adhesion pathways. Eleven significantly enriched transcription factor motifs (PAX5, EGR1, XBP1, SREBP1, OLF1, MZF1, NFY, NFKAPPAB, MYCMAX, NFE2, and RP58) were identified. The DEGs and transcription factor motifs identified in our study provide biomarkers for the understanding of Down syndrome pathogenesis and progression.
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spelling pubmed-41812182014-10-15 Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome Kong, X.D. Liu, N. Xu, X.J. Braz J Med Biol Res Biomedical Sciences In this study, biomarkers and transcriptional factor motifs were identified in order to investigate the etiology and phenotypic severity of Down syndrome. GSE 1281, GSE 1611, and GSE 5390 were downloaded from the gene expression ominibus (GEO). A robust multiarray analysis (RMA) algorithm was applied to detect differentially expressed genes (DEGs). In order to screen for biological pathways and to interrogate the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, the database for annotation, visualization, and integrated discovery (DAVID) was used to carry out a gene ontology (GO) function enrichment for DEGs. Finally, a transcriptional regulatory network was constructed, and a hypergeometric distribution test was applied to select for significantly enriched transcriptional factor motifs. CBR1, DYRK1A, HMGN1, ITSN1, RCAN1, SON, TMEM50B, and TTC3 were each up-regulated two-fold in Down syndrome samples compared to normal samples; of these, SON and TTC3 were newly reported. CBR1, DYRK1A, HMGN1, ITSN1, RCAN1, SON, TMEM50B, and TTC3 were located on human chromosome 21 (mouse chromosome 16). The DEGs were significantly enriched in macromolecular complex subunit organization and focal adhesion pathways. Eleven significantly enriched transcription factor motifs (PAX5, EGR1, XBP1, SREBP1, OLF1, MZF1, NFY, NFKAPPAB, MYCMAX, NFE2, and RP58) were identified. The DEGs and transcription factor motifs identified in our study provide biomarkers for the understanding of Down syndrome pathogenesis and progression. Associação Brasileira de Divulgação Científica 2014-08-08 /pmc/articles/PMC4181218/ /pubmed/25118625 http://dx.doi.org/10.1590/1414-431X20143792 Text en
spellingShingle Biomedical Sciences
Kong, X.D.
Liu, N.
Xu, X.J.
Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title_full Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title_fullStr Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title_full_unstemmed Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title_short Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome
title_sort bioinformatics analysis of biomarkers and transcriptional factor motifs in down syndrome
topic Biomedical Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181218/
https://www.ncbi.nlm.nih.gov/pubmed/25118625
http://dx.doi.org/10.1590/1414-431X20143792
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