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BMC Genomics. 2015 Aug 28;16:645. doi: 10.1186/s12864-015-1785-9.

MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data.

Author information

1
Charité - Universitätsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies (BCRT), Berlin, 13353, Germany. khadija.el-amrani@charite.de.
2
Charité - Universitätsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies (BCRT), Berlin, 13353, Germany. Harald.Stachelscheid@charite.de.
3
Berlin Institute of Health, Berlin, 10117, Germany. Harald.Stachelscheid@charite.de.
4
Charité - Universitätsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies (BCRT), Berlin, 13353, Germany. Fritz.Lekschas@charite.de.
5
Charité - Universitätsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies (BCRT), Berlin, 13353, Germany. Andreas.Kurtz@charite.de.
6
Seoul National University, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul, 151-742, Republic of Korea. Andreas.Kurtz@charite.de.
7
Faculty of Biology, Johannes Gutenberg University of Mainz, Mainz, Germany. andrade@uni-mainz.de.
8
Institute of Molecular Biology, Mainz, Germany. andrade@uni-mainz.de.

Abstract

BACKGROUND:

Identification of marker genes associated with a specific tissue/cell type is a fundamental challenge in genetic and cell research. Marker genes are of great importance for determining cell identity, and for understanding tissue specific gene function and the molecular mechanisms underlying complex diseases.

RESULTS:

We have developed a new bioinformatics tool called MGFM (Marker Gene Finder in Microarray data) to predict marker genes from microarray gene expression data. Marker genes are identified through the grouping of samples of the same type with similar marker gene expression levels. We verified our approach using two microarray data sets from the NCBI's Gene Expression Omnibus public repository encompassing samples for similar sets of five human tissues (brain, heart, kidney, liver, and lung). Comparison with another tool for tissue-specific gene identification and validation with literature-derived established tissue markers established functionality, accuracy and simplicity of our tool. Furthermore, top ranked marker genes were experimentally validated by reverse transcriptase-polymerase chain reaction (RT-PCR). The sets of predicted marker genes associated with the five selected tissues comprised well-known genes of particular importance in these tissues. The tool is freely available from the Bioconductor web site, and it is also provided as an online application integrated into the CellFinder platform ( http://cellfinder.org/analysis/marker ).

CONCLUSIONS:

MGFM is a useful tool to predict tissue/cell type marker genes using microarray gene expression data. The implementation of the tool as an R-package as well as an application within CellFinder facilitates its use.

PMID:
26314578
PMCID:
PMC4552366
DOI:
10.1186/s12864-015-1785-9
[Indexed for MEDLINE]
Free PMC Article

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