Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Jan 15:10:20.
doi: 10.1186/1471-2105-10-20.

Detecting intergene correlation changes in microarray analysis: a new approach to gene selection

Rui Hu  1 , Xing Qiu, Galina Glazko, Lev Klebanov, Andrei Yakovlev
Affiliations

Detecting intergene correlation changes in microarray analysis: a new approach to gene selection

Rui Hu et al. BMC Bioinformatics. .

Abstract

Background: Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (differentially correlated genes). We intend to enrich the above procedure by proposing a nonparametric selection procedure that selects differentially correlated genes.

Results: Using both simulations and resampling techniques, we found that our procedure correctly detected genes that were not differentially expressed but differentially correlated. We also applied our procedure to a set of biological data and found some potentially important genes that were not selected by the traditional method.

Discussion and conclusion: Microarray technology yields multidimensional information on the function of the whole genome. Rather than treating intergene correlation as a nuisance to the traditional gene selection procedures which are essentially univariate, our method utilizes the rich information contained in the correlation as a new selection criterion. It can provide additional useful candidate genes for the biologists.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Estimated Null Density Functions (resampling method with Bonferroni threshold 0.05) without shuffling slides, the estimated N-statistic is 173.83 for the significant gene and 25.74 for the non-significant gene. The estimated density functions of most other genes follow the same pattern.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Dudoit S, Shaffer J, Boldrick J. Multiple hypothesis testing in microarray experiments. Statistical Science. 2003;18:71–103.
    1. Simon RM, Korn EL, McShane LM, Radmacher MD, Wright GW, Zhao Y. Design and Analysis of DNA Microarray Investigations. Springer Verlag; 2003.
    1. Klebanov L, Jordan C, Yakovlev A. A new type of stochastic dependence revealed in gene expression data. Stat Appl Genet Mol Biol. 2006;5:Article7. - PubMed
    1. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA. 2005;102:13544–13549. - PMC - PubMed
    1. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing JR. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. 2002;1:133–143. - PubMed

Publication types

MeSH terms

LinkOut - more resources