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Open Access Research article

Genomic expression during human myelopoiesis

Francesco Ferrari1, Stefania Bortoluzzi2, Alessandro Coppe2, Dario Basso3, Silvio Bicciato3, Roberta Zini1, Claudia Gemelli1, Gian Antonio Danieli2 and Sergio Ferrari1*

Author Affiliations

1 Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy

2 Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy

3 Department of Chemical Engineering Processes, University of Padova via F. Marzolo 9, 35131, Padova, Italy

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BMC Genomics 2007, 8:264  doi:10.1186/1471-2164-8-264

Published: 3 August 2007

Abstract

Background

Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization.

Results

Gene expression data from 24 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset of 9,425 genes, each reliably associated to a unique genomic position and chromosomal coordinate. Lists of genes constitutively expressed or silent during myelopoiesis and of genes differentially expressed in commitment phase of myelopoiesis were first identified using a classical data analysis procedure. Then, the genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. This approach allowed identifying specific chromosomal regions significantly highly or weakly expressed, and clusters of differentially expressed genes and of transcripts related to specific functional modules.

Conclusion

The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.