Download Identification of Tissue Specific Transcription Factors Using

Identification of Tissue Specific Transcription Factors Using
Microarray Gene Expression Data
Larisa Kiseleva1
Ekaterina Shelest2
[email protected]
[email protected]
Edgar Wingender2,3
[email protected]
1
2
3
Paul Horton1
[email protected]
Computational Biology Research Center, AIST Waterfront Bio-IT Research Building, 2-42 Aomi,
Koto-ku, Tokyo 135-0064, Japan
Department of bioinformatics, UKG, University of Goettingen, Goldschmidtstrasse 1, D-37077
Goettingen, Germany
BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbuttel, Germany
Keywords : transcription factors, tissue specific gene expression, microarray analysis
1 Introduction
Tissue specific transcription factors play an essential role in establishing cell identity during development.
Using microarray gene expression data for 78 human cell/tissue types we characterized expression
features of available transcription factors. As a result, we obtained a list of transcription factors whose
expression is specific to one or more tissues, suggesting their role in the regulation of cell-type specific genes.
2
Method and Results
Microarray data was retrieved from the Gene Expression Omnibus database, GDS596 [1, 2]. In total 1590
probes covering 810 genes encoding transcription factors were taken for the analysis. For every probe we made
a plot showing its expression profile for 78 cell/tissue types. We classified all the profiles into three major
groups. The first and largest group contains genes that show ubiquitous expression in the analyzed tissues
(Figure 1). The second group contains tissue-specific genes. We identified transcription factor coding genes with
increased expression level in certain organs or tissues: brain, liver, colon, testis, prostate, muscle cells, thyroid,
adrenal gland etc. Since some of the tissue categories are not mutually exclusive, for example brain, cerebellum,
amygdala, pons, tissue specific genes can be further subdivided into those characteristic for the whole organ
(Figure 2) or expressed in its specific parts (Figure3). And the third group contains genes showing increased
expression value in several distinct tissues (Figure 4).
Figure 1: Expression values of AHR
Figure 2: Expression values of ARNT2
Figure 3: Expression values of ZIC1
Figure 4: Expression values of TITF1
3
Discussion
This research can be extended to the identification of regulatory targets of tissue specific transcription factors,
which will help to reveal tissue-specific gene regulatory networks. This, in turn, can yield insights into the
molecular basis of a tissue's development, function and pathology.
References
[1] Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa,
M., Kreiman, G., Cooke, M.P., Walker, J.R., and Hogenesch, J.B., A gene atlas of the mouse and
human protein-encoding transcriptomes, Proc. Natl. Acad. Sci. USA, 101(16):6062-6067, 2004.
[2] http: / www.ncbi.nlm.nih.gov/geo/