A WWW supplement to:
Yitzhak (Tzachi) Pilpel*
Priya Sudarsanam*
George M. Church
*These authors made equal contributions to this work
Department of Genetics, Harvard Medical School, and
Lipper Center for Computational
Genetics
Abstract
The recent availability of microarray data has led to the development of several computational approaches for studying genome-wide transcriptional regulation. However, few studies have addressed the combinatorial nature of transcription, a well-establishe
d phenomenon in eukaryotes. We have developed a new computational method that analyzes microarray data to discover synergistic motif combinations in the promoters of S. cerevisiae. Our method suggests causal relationships between each motif in a combinati
on and the overall coherence of the observed expression patterns. In addition to identifying novel motif combinations that affect expression patterns during the cell cycle, sporulation, and various stress response conditions, we have also discovered regul
atory cross-talk between several of these processes. We have generated motif synergy maps that provide a global view of the transcription networks in the cell. The maps are highly connected suggesting that a small number of transcription factors are respo
nsible for a complex set of expression patterns in diverse conditions. This approach should be important and applicable for modeling transcriptional regulatory networks in more complex eukaryotes.
Figures
General
Figure 1AB: General Flaw Chart Scheme
Figure 2: The effect of motif orientation on expression cohernece
Motif interaction maps
Figure 3: A Global Map of Motif Synergy
Supplementary interaction maps:
The ribosomal regulatory elements map
Combinograms
Figure4AB: cell cycle and sporulation
Figure5AB: heat shock and DNA damaging agents
Supplementary Combinograms:
diauxic shift
dtt treatment
cold shock
Parameter Landscape Analyses
Investigate here the effect of different choices of analyses parameters
Tables
A collection of known and putative motifs
Expression Coherence Score of individual motifs
Synergistic Motif Pairs
Data & Resources
All expression data were
taken from ExpressDB
Motifs were derived using AlignACE
and matched to promoters in the genome using ScanACE
Contacts
Correspondence may be addressed to George M. Church at:
Department of Genetics,
Harvard Medical School
200 Longwood Avenue,
Boston, MA 02115 USA
fax (617) 432-7266
Or Email to:
Tzachi Pilpel
Priya Sudarsanam
George Church