[Colloquium] TTIC Colloquium: Sheng Zhong, UIUC

[Julia MacGlashan]

When:             *Monday, Nov 1 @ 1:00pm*

Where:           * TTIC Conference Room #526*, 6045 S Kenwood Ave, 5th Floor

Who:              * Sheng Zhong*, UIUC

Title:               * Network based comparison of temporal gene expression
patterns *


In the pursuits of mechanistic understanding of cell differentiation, it is
often necessary to compare multiple differentiation processes triggered by
different external stimuli and internal perturbations. Available methods for
comparing temporal gene expression patterns are limited to a gene-by-gene
approach, which ignores co-expression information and thus is sensitive to
measurement noise. We present a method for co-expression network based
comparison of temporal expression patterns (NACEP). NACEP compares the
temporal patterns of a gene between two experimental conditions, taking into
consideration all of the possible co-expression modules that this gene may
participate in. NACEP first uses a Dirichlet Process to cluster genes, and
then it uses probabilistically averaged spline curves to compare temporal
patterns. We applied NACEP to analyze RA-induced differentiation of
embryonic stem (ES) cells. The analysis suggests RA may facilitate neural
differentiation by inducing the shh and insulin receptor pathways. NACEP was
also applied to compare the temporal responses of seven RNA inhibition
(RNAi) experiments. As proof of concept, we demonstrate that the difference
in the temporal responses to RNAi treatments can be used to derive
interaction relationships of transcription factors (TFs), and therefore
infer regulatory modules within a transcription network. In particular, the
analysis suggested a novel regulatory relationship between two pluripotency
regulators, Esrrb and Tbx3, which was supported by in vivo binding of Esrrb
to the promoter of Tbx3.

Host:             Jinbo Xu, j3xu at ttic.edu
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