Continuous hidden process model for time series expression experiments

Yanxin Shi, Michael Klutstein, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Motivation: When analyzing expression experiments, researchers are often interested in identifying the set of biological processes that are up-or down-regulated under the experimental condition studied. Current approaches, including clustering expression profiles and averaging the expression profiles of genes known to participate in specific processes, fail to provide an accurate estimate of the activity levels of many biological processes. Results: We introduce a probabilistic continuous hidden process Model (CHPM) for time series expression data. CHPM can simultaneously determine the most probable assignment of genes to processes and the level of activation of these processes over time. To estimate model parameters, CHPM uses multiple time series datasets and incorporates prior biological knowledge. Applying CHPM to yeast expression data, we show that our algorithm produces more accurate functional assignments for genes compared to other expression analysis methods. The inferred process activity levels can be used to study the relationships between biological processes. We also report new biological experiments confirming some of the process activity levels predicted by CHPM.

Original languageAmerican English
Pages (from-to)i459-i467
Issue number13
StatePublished - 1 Jul 2007

Bibliographical note

Funding Information:
This work was supported in part by NIH grant NO1 AI-5001 and NSF CAREER award 0448453 to Z.B.J.


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