Jan Komorowski, Professor of Bioinformatics
Program in Computational and Systems Biology
Department of Cell and Molecular Biology
Institute of Computer Science, PAN, Warsaw
On 17 maj 2014, at 22:14, Mark Gerstein <firstname.lastname@example.org> wrote:
> 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. We 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. In particular:
> (1) We developed 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. They
> were then used to align the stages in worm and fly development,
> finding the normal embryo-to-embryo and larvae-to-larvae pairings in
> addition to a novel pairing between worm embryo and fly pupae.
> (2) We developed a global optimization algorithm to examine the
> hierarchical organization of the regulatory network. We found that,
> despite extensive rewiring of binding targets, high-level organization
> principles such as a three-layer heirarchy are conserved across the
> three species.
> (3) We found 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 expressionlevel for both protein
> coding genes and ncRNAs.
> (4) Finally, we found that the extent of the non-coding, non-canonical
> transcription is consistent between worm, fly and human.