STAT SEMINAR SERIES :: Gene number estimation and gene capture prediction in EST sequencing

Event Details
  • Date/Time:
    • Tuesday April 4, 2006
      12:30 pm - 12:00 am
  • Location: Executive Room #228
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Contact
Barbara Christopher
Industrial and Systems Engineering
Contact Barbara Christopher
404.385.3102
Summaries

Summary Sentence: STAT SEMINAR SERIES :: Gene number estimation and gene capture prediction in EST sequencing

Full Summary: STAT SEMINAR SERIES :: Gene number estimation and gene capture prediction in EST sequencing

In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experimental design, as well as clues to the diversity of expressed genes in the tissue from which the library was constructed. We propose a compound Poisson process model that can accurately predict the gene capture in a future EST sample based on an initial EST sample. It also allows estimation of the number of expressed genes in one cDNA library or co-expressed in two cDNA libraries. The superior performance of the new prediction method over an existing approach is established by a simulation study. Our analysis of four Arabidopsis thaliana EST sets suggests that the number of expressed genes present in four different cDNA libraries of Arabidopsis thaliana varies from 9155 (root) to 12005 (silique). An observed fraction of co-expressed genes in two different EST sets as low as 25% can correspond to an actual overlap fraction greater than 65%.

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School of Industrial and Systems Engineering (ISYE)

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Status
  • Created By: Barbara Christopher
  • Workflow Status: Published
  • Created On: Oct 8, 2010 - 7:35am
  • Last Updated: Oct 7, 2016 - 9:52pm