Institute of Information Science Academia Sinica
Topic: TIGP--Modeling and Comparing the Organization of Circular Genomes
Speaker: Dr. Grace S. Shieh (Institute of Statistical Science, Academia Sinica)
Date: 2012-05-31 (Thu) 14:00 – 15:30
Location: Auditorium 106 at new IIS Building
Host: Miss Elsa Pan

Abstract:

Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial

genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. This motivated us to develop a family of bivariate distributions and its statistical inference. A new measure is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria which are mammalian pathogens. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites between any pair of circular genomes and genome construction in synthetic biology.

Lab presentation:

To develop therapeutics specific to cancer cells, we have applied the concept of synthetic lethality, and analyzed gene expression data of colorectal cancer (CRC) and normal tissues, which has resulted a panel of gene pairs which are involved in maintaining tumor status. Further, we obtained these pairs' IHC protein expression, and found protein pairs which are correlated to certain clinical factors of CRC patients, e.g. tumor size and prognosis. Finally, gene pairs which have synergistic effects in maintaining tumor status and RNAi results on killing tumor cells via cell line HCT-15 will be reported.