Saturday, August 30, 2014

Re: Abstract for SAMSI meeting, Opening workshop '14 (i0samsi)

Abstract for

Human Genome Analysis

The ENCODE and modENCODE consortia have generated a resource
containing large amounts of transcriptomic data, extensive mapping of
chromatin states, as well as the binding locations of over 300
transcription-regulatory factors for human, worm and fly. The consortium performed
extensive data integration by constructing genome-wide co-expression
networks and transcriptional regulatory models, revealing fundamental
principles of transcription and network organization that are
conserved across the three highly divergent animals. 

I will give an overview of the data and some of the key analyses. 
In particular:

(1) A novel cross-species clustering algorithm to
integrate the co-expression networks of the three species, resulted at
conserved modules shared between the organisms. These modules are
enriched in developmental genes and exhibited hourglass behavior. 

(2) A global optimization algorithm to examine the
hierarchical organization of the regulatory network. 
Despite extensive rewiring of binding targets, high-level organization
principles such as a three-layer heirarchy are conserved across the
three species.

(3) The gene expression levels in the organisms, both coding
and non-coding, can be predicted consistently based on their upstream
histone marks. In fact, a "universal model" with a single set of
cross-organism parameters can predict expression level for both protein
coding genes and ncRNAs.

(4) Their have been many analyses of pseudogenes. 

(5) Finally, the extent of the non-coding, non-canonical
transcription is consistent between worm, fly and human.

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