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Using microarray analysis to identify genes and pathways that regulate fetal hemoglobin levels

Using microarray analysis to identify genes and pathways that regulate fetal hemoglobin levels Increased levels of fetal hemoglobin (HbF: α2γ2) can ameliorate the clinical severity of the β‐hemoglobinopathies. Microarray analysis represents a powerful approach to identify novel genetic factors regulating the γ‐globin gene. Gene expression profiling was previously performed on 14 individuals with high or normal HbF levels to identify the genetic factors that control γ‐globin gene expression. To obtain more accurate and reliable results, our results were combined with public microarray dataset GSE22109 deposited in the Gene Expression Omnibus database. Annotation of case versus control samples was taken directly from the microarray documentation. The differentially expressed genes (DEGs) were obtained and were deeply analyzed by bioinformatics methods. Combined with our own chip expression data, potential genes HBE1, TFRC, and CSF2 were selected out for subsequent qRT‐PCR validation. A total of 184 DEGs were identified from GSE22109 and the protein–protein interaction network was constructed. Gene set enrichment analysis showed that the hematopoietic cell lineage pathway overlaps in the two datasets. HBE1, CSF2, and TFRC were confirmed by qRT‐PCR. Our results suggest novel candidate genes and pathways associated with the γ‐globin gene expression. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Annals of Human Genetics Wiley

Using microarray analysis to identify genes and pathways that regulate fetal hemoglobin levels

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References (39)

Publisher
Wiley
Copyright
© 2020 John Wiley & Sons Ltd/University College London
ISSN
0003-4800
eISSN
1469-1809
DOI
10.1111/ahg.12346
Publisher site
See Article on Publisher Site

Abstract

Increased levels of fetal hemoglobin (HbF: α2γ2) can ameliorate the clinical severity of the β‐hemoglobinopathies. Microarray analysis represents a powerful approach to identify novel genetic factors regulating the γ‐globin gene. Gene expression profiling was previously performed on 14 individuals with high or normal HbF levels to identify the genetic factors that control γ‐globin gene expression. To obtain more accurate and reliable results, our results were combined with public microarray dataset GSE22109 deposited in the Gene Expression Omnibus database. Annotation of case versus control samples was taken directly from the microarray documentation. The differentially expressed genes (DEGs) were obtained and were deeply analyzed by bioinformatics methods. Combined with our own chip expression data, potential genes HBE1, TFRC, and CSF2 were selected out for subsequent qRT‐PCR validation. A total of 184 DEGs were identified from GSE22109 and the protein–protein interaction network was constructed. Gene set enrichment analysis showed that the hematopoietic cell lineage pathway overlaps in the two datasets. HBE1, CSF2, and TFRC were confirmed by qRT‐PCR. Our results suggest novel candidate genes and pathways associated with the γ‐globin gene expression.

Journal

Annals of Human Genetics – Wiley

Published: Jan 1, 2020

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