GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.
BACKGROUND
Macrophages play an integral role in the host immune system, bridging innate and adaptive immunity. As such, they are finely attuned to extracellular and intracellular stimuli and respond by rapidly initiating multiple signalling cascades with diverse effector functions. The macrophage cell is therefore an experimentally and clinically amenable biological system for the mapping of biological pathways. The goal of the macrophage expression atlas is to systematically investigate the pathway biology and interaction network of macrophages challenged with a variety of insults, in particular via infection and activation with key inflammatory mediators. As an important first step towards this we present a single searchable database resource containing high-throughput macrophage gene expression studies.


METHODS
The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for gene expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX-MEA follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the searching of expression data from different microarray experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the research community.


CONCLUSIONS
GPX-MEA is the first example of a quality scored gene expression database focussed on a macrophage cellular system that allows efficient identification of transcriptional patterns. The resource will provide novel insights into the phenotypic response of macrophages to a variety of benign, inflammatory, and pathogen insults. GPX-MEA is available through the GPX website at http://www.gti.ed.ac.uk/GPX.
Grimes
Graeme R
GR
The Scottish Centre for Genomic Technology and Informatics, University Of Edinburgh, 49 Little France Crescent, Edinburgh, EH16 4SB, UK. Graeme.Grimes@ed.ac.uk
Moodie
Stuart
S
Beattie
John S
JS
Craigon
Marie
M
Dickinson
Paul
P
Forster
Thorsten
T
Livingston
Andrew D
AD
Mewissen
Muriel
M
Robertson
Kevin A
KA
Ross
Alan J
AJ
Sing
Garwin
G
Ghazal
Peter
P
D000818:Animals; D019295:Computational Biology; D003625:Data Collection; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D008264:Macrophages / Q000737:chemistry*; D046228:Microarray Analysis / Q000379:methods; D011786:Quality Control; D012107:Research Design; D012985:Software Design