N-terminal tails of H2A, H2B, H3 and H4 histone families are subjected to 
posttranslational modifications that take part in transcriptional regulation 
mechanisms, such as transcription factor binding and gene expression. Regulation 
mechanisms under control of histone modification are important but remain 
largely unclear, despite of emerging datasets for comprehensive analysis of 
histone modification. In this paper, we focus on what we call genetic harmonious 
units (GHUs), which are co-occurring patterns among transcription factor 
binding, gene expression and histone modification. We present the first 
genome-wide approach that captures GHUs by combining ChIP-chip with microarray 
datasets from Saccharomyces cerevisiae. Our approach employs noise-robust soft 
clustering to select patterns which share the same preferences in transcription 
factor-binding, histone modification and gene expression, which are all 
currently implied to be closely correlated. The detected patterns are a 
well-studied acetylation of lysine 16 of H4 in glucose depletion as well as 
co-acetylation of five lysine residues of H3 with H4 Lys12 and H2A Lys7 
responsible for ribosome biogenesis. Furthermore, our method further suggested 
the recognition of acetylated H4 Lys16 being crucial to histone 
acetyltransferase ESA1, whose essential role is still under controversy, from a 
microarray dataset on ESA1 and its bypass suppressor mutants. These results 
demonstrate that our approach allows us to provide clearer principles behind 
gene regulation mechanisms under histone modifications and detect GHUs further 
by applying to other microarray and ChIP-chip datasets. The source code of our 
method, which was implemented in MATLAB (http://www.mathworks.com/), is 
available from the supporting page for this paper: 
http://www.bic.kyoto-u.ac.jp/pathway/natsume/hm_detector.htm.