Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge

Wentao Zhao, Erchin Serpedin, Edward R. Dougherty

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological processes, for example, cell cycle and circadian rhythm. The power of a scheme is practically measured by comparing the detected periodically expressed genes with experimentally verified genes participating in a cyclic process. However, in the above mentioned procedure the valuable prior knowledge only serves as an evaluation benchmark, and it is not fully exploited in the implementation of the algorithm. In addition, partial data sets are also disregarded due to their nonstationarity. This paper proposes a novel algorithm to identify cyclic-process-involved genes by integrating the prior knowledge with the gene expression analysis. The proposed algorithm is applied on data sets corresponding to Saccharomyces cerevisiae and Drosophila melanogaster, respectively. Biological evidences are found to validate the roles of the discovered genes in cell cycle and circadian rhythm. Dendrograms are presented to cluster the identified genes and to reveal expression patterns. It is corroborated that the proposed novel identification scheme provides a valuable technique for unveiling pathways related to cyclic processes.

Original languageEnglish
Article number683463
JournalEurasip Journal on Bioinformatics and Systems Biology
Volume2009
DOIs
Publication statusPublished - 2009
Externally publishedYes

Fingerprint

Gene Expression Analysis
Prior Knowledge
Gene expression
Genes
Gene
Gene Expression
Circadian Rhythm
Cell Cycle
Biological Phenomena
Benchmarking
cdc Genes
Periodicity
Cells
Multigene Family
Drosophila melanogaster
Dendrogram
Identification Scheme
Saccharomyces cerevisiae
Nonstationarity
Drosophilidae

ASJC Scopus subject areas

  • Medicine(all)
  • Computer Science(all)
  • Signal Processing
  • Statistics and Probability
  • General

Cite this

Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge. / Zhao, Wentao; Serpedin, Erchin; Dougherty, Edward R.

In: Eurasip Journal on Bioinformatics and Systems Biology, Vol. 2009, 683463, 2009.

Research output: Contribution to journalArticle

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