1. Diverse patterns, similar mechanismwt
cic-
zen
tll
hkb
Jimenez G. et al. 2000 wt
tor+ oc
Gao Q. and Finkelstein R, 1998
There is an enrichment of cic binding sites in the known enhancers for this set of genes

2. Operations are used to construct more complex patterns
Combinatorial representation of spatial expression patterns
Data mining: Identifying primitives
Primitives reflect inductive signals
Shvartsman et al. 2008
Operations are used to construct more complex patterns
Input:
primitives
The geometric models provide a framework to connect inductive signals to gene regulation

3. Integration of ChIP data for regulatory module prediction
Anterior-Posterior
Dorsal-Ventral
False positive
CRM predictions
Berman 2004
AP negatives
Ochoa-Espinosa 2005
DV negatives
Markstein 2004
Classic experiments and binding site clustering models have provided ~100 cis regulatory modules (CRMs) for the early embryonic patterning. ChIP experiments, with chromatin marks and evolutionary signatures, can be used to predict additional CRMs

4. Statistics on TFs compared to all genes
Embryonic spatial profiling of all transcription factors w/ Sue Celniker BDGP
TF counts
569 TF annotated (78% of 731 total)
511 are expressed
370 show tissue/organ expression
Statistics on TFs compared to all genes
Comparison of fraction of genes
expressed at a stage
Comparison # of stage
expressed per gene
TFsstage / TFsembryo
Genesstage / Genesembryo
Fold enrichment (log2)
Fold enrichment (log2)
Developmental stage range
Number of stages expressed

5. Organ system TF enrichments
Time
Time
-2.5
2.5
Time
Log2(enrichment)
TFstissue / Genestissue
TFsembryo / Genesembryo