Diverse patterns, similar mechanism

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Presentation transcript:

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

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

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

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

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