Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome.

Abstract

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.

• Authors: X D Kong, N Liu, X J Xu
• Journal: Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas (Braz J Med Biol Res) Vol. 47 Issue 10 Pg. 834-41 (Oct 2014) ISSN: 1414-431X [Electronic] Brazil
• PMID: 25118625 (Publication Type: Journal Article)

Chemical References

• Biomarkers
• Transcription Factors

Topics

• Algorithms
• Amino Acid Motifs (genetics)
• Animals
• Biomarkers (analysis)
• Computational Biology (methods)
• Databases, Genetic
• Down Syndrome (etiology, genetics)
• Gene Expression
• Gene Ontology
• Gene Regulatory Networks (genetics)
• Humans
• Mice
• Molecular Sequence Annotation (methods)
• Phenotype
• Protein Array Analysis (methods)
• Rats
• Transcription Factors (analysis)
• Up-Regulation (genetics)