Transcript Slide 1
Diverse patterns, similar mechanism wt 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 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 Integration of ChIP data for regulatory module prediction Dorsal-Ventral False positive CRM predictions DV negatives Berman 2004 Ochoa-Espinosa 2005 Markstein 2004 AP negatives Anterior-Posterior 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 Embryonic spatial profiling of all transcription factors w/ Sue Celniker BDGP TF counts Maternal s1-3 332 • 569 TF annotated (78% of 731 total) • 511 are expressed • 370 show tissue/organ expression s4-6 144 Tissue / Organ system s7-8 s9-10 s11-12 172 208 283 s13-16 345 s4-6 100 s7-8 75 Ubiquitous s9-10 s11-12 76 73 s13-16 50 Statistics on TFs compared to all genes Comparison # of stage expressed per gene Fold enrichment (log2) Fold enrichment (log2) Genesstage / Genesembryo TFsstage / TFsembryo Comparison of fraction of genes expressed at a stage Developmental stage range Number of stages expressed Time Time Time Organ system TF enrichments -2.5 2.5 Log2(enrichment) TFstissue / Genestissue TFsembryo / Genesembryo