Diverse patterns, similar mechanism

wt cic-

tor+

tll

hkb

zen

oc

wt

There is an enrichment of cic binding sites in the known enhancers for this set of genes

Jimenez G. et al. 2000

Gao Q. and Finkelstein R, 1998

Combinatorial representation of spatial expression patterns

Operations are used to construct more complex patterns

Data mining: Identifying primitives

Shvartsman et al. 2008

Primitives reflect inductive signals

The geometric models provide a framework to connect inductive signals to gene regulation

Input:primitives

Integration of ChIP data for regulatory module prediction

Anterior-Posterior Dorsal-Ventral

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

Berm

an 2004M

arkstein 2004

Ochoa-E

spinosa 2005

DV

neg

ativ

esA

P n

egat

ives

False positive CRM predictions

Embryonic spatial profiling of all transcription factorsw/ Sue Celniker BDGP

• 569 TF annotated (78% of 731 total)• 511 are expressed• 370 show tissue/organ expression

Maternals1-3 s4-6 s7-8 s9-10 s11-12 s13-16332 144 172 208 283 345

s4-6 s7-8 s9-10 s11-12 s13-16100 75 76 73 50

Tissue / Organ system

Ubiquitous

TF counts

Fol

d en

richm

ent

(log

2)

Fol

d en

richm

ent

(log

2)

Developmental stage range Number of stages expressed

TF

s sta

ge /

TF

s em

bryo

Ge

ne

s sta

ge /

Ge

ne

s em

bryo

Comparison of fraction of genesexpressed at a stage

Comparison # of stage expressed per gene

Statistics on TFs compared to all genes

-2.5 2.5

Log2(enrichment)

TFstissue / Genestissue

TFsembryo / Genesembryo

Tim

e

Tim

e

Tim

e

Organ system TF enrichments