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

Background The 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 correl...

Celý popis

Uložené v:
Podrobná bibliografia
Vydané v:BMC genomics Ročník 14; číslo 1; s. 632
Hlavní autori: Mabbott, Neil A, Baillie, J Kenneth, Brown, Helen, Freeman, Tom C, Hume, David A
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 20.09.2013
BioMed Central Ltd
Springer Nature B.V
Predmet:
Animal Genetics and Genomics
Anopheles
Arrays
B cells
Biomedical and Life Sciences
Cluster Analysis
Computational Biology
Data processing
Dendritic cells
Dendritic Cells - metabolism
DNA binding proteins
Gene expression
Gene Regulatory Networks
Genetic aspects
Genetic regulation
Genomes
Genomics
Human and rodent genomics
Humans
Life Sciences
Macrophages - metabolism
Meta-analysis
Microarrays
Microbial Genetics and Genomics
Oligonucleotide Array Sequence Analysis
Ontology
Phagocytes
Physiological aspects
Plant Genetics and Genomics
Proteomics
Quality control
Research Article
Stem cells
Transcription factors
Transcription Factors - genetics
Transcriptome
Human
Primary cells
Dendritic cell
Transcriptomics
Clustering
Microarray
Meta-analysis
Macrophage
ISSN:1471-2164, 1471-2164
On-line prístup:Získať plný text
Tagy: Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
Popis
Shrnutí:Background The 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. Results Using the network analysis tool BioLayout Express 3D 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. Conclusions We 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 ).
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
ObjectType-Article-2
ObjectType-Feature-1
content type line 23
ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-14-632