Identification of Differentially Expressed Transcripts using Next Generation Sequencing Technology and Integration of Multiple Genomic Assays using Partek Genomics Suite

Speaker: Mike Lelivelt, Ph.D., Vice President of Genomics, Partek Inc.

Location: Room 601A, Becker Medical Library

Time: 1:30 PM – 3:00 PM, Thursday, October 15, 2009

Abstract:

As genomic technologies continue to evolve, the scope and size of both genomic and transcriptomic data increases and the importance of approachable analysis solutions continues to grow.  Partek Genomics Suite continues to grow and evolve to match the changes available in today’s genomic technologies.  In this seminar, an overview of the current capabilities of Partek will be presented with a special focus on analysis methods for mRNA-seq as well as ChIP-seq for Next Generation Sequencing technologies.  Quantitation of mRNA-seq produces a table of predicted transcripts with relative abundances of each transcript.  This shift from a gene-centered data table to a transcript-centered data table should significantly increase the information content of expression studies. Also available in the mRNA-seq workflow is a method to identify novel exons/transcript that are currently unmapped in the NCBI mRNA space.  In addition to mRNA-seq, Partek supports full analysis workflows for ChIP-seq including peak identification as well as motif discovery across regions of bound proteins.

The increase in the number of large scale genomic assays available to researchers has lead to an increase in researchers running samples on multiple assays and then wanting to integrate both data types together. Partek has developed workflows to integrate several different assays with gene expression data.  Within the seminar, we will demonstrate how either copy number, ChIP-chip/ChIP-seq, or microRNA studies can be integrated with gene expression data.