An expression atlas of human primary cells: inference of gene function from coexpression networksReport as inadecuate




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BMC Genomics

, 14:632

Human and rodent genomics

Abstract

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 Express 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.

KeywordsClustering Meta-analysis Human Primary cells Dendritic cell Macrophage Microarray Transcriptomics AbbreviationsBMBone marrow

DCDendritic cell

ESEmbryonic stem

G-CSFGranulocyte colony-stimulating factor

GM-CSFGranulocyte-macrophage colony-stimulating factor

GOGene ontology

HLAHuman leukocyte antigen

IFNInterferon

iPS cellInduced pluripotent stem cell

LPSLipopolysaccharide

MCLMarkov clustering

MHCMajor histocompatibility complex

pDCPlasmacytoid dendritic cell

QCQuality control

RMARobust multi-array average

TLRToll-like receptor.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-632 contains supplementary material, which is available to authorized users.

Neil A Mabbott, Tom C Freeman and David A Hume contributed equally to this work.

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Author: Neil A Mabbott - J Kenneth Baillie - Helen Brown - Tom C Freeman - David A Hume

Source: https://link.springer.com/







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