An expression atlas of human primary cells: inference of gene function from coexpression networks

BMC Genomics

Research Article

J Kenneth Baillie¹  Helen Brown¹  David A Hume¹  Tom C Freeman¹  Neil A Mabbott¹ 

[1] The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, EH25 9RG, Midlothian, Edinburgh, UK;

关键词: Clustering;    Meta-analysis;    Human;    Primary cells;    Dendritic cell;    Macrophage;    Microarray;    Transcriptomics;   

DOI  :  10.1186/1471-2164-14-632

 received in 2013-03-19, accepted in 2013-06-25,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets derived from human primary cells and analysed large correlation graphs of these data.ResultsUsing the network analysis tool BioLayout Express3D we identify robust co-associations of genes expressed in a wide variety of cell lineages. We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control.ConclusionsWe consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system. Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (http://biogps.org/dataset/2429/primary-cell-atlas/) and on macrophages.com (http://www.macrophages.com/hu-cell-atlas).

【 授权许可】

CC BY   
© Mabbott et al.; licensee BioMed Central Ltd. 2013