|Table of Contents|

Clustering GO Terms Applied to Differential Gene Expression Detection(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

Issue:
2011 03
Page:
422-426
Research Field:
T & M
Publishing date:

Info

Title:
Clustering GO Terms Applied to Differential Gene Expression Detection
Author(s):
TANG Qiuju XU Tao WANG Dong LI Lingjin DU Linfang
(1Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China)
(2Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, Chengdu 610041, China)
Keywords:
gene ontology hierarchy clustering differential gene expression semantic similarity
CLC:
Q811.4
PACS:
DOI:
10.3724/SP.J.1145.2011.00422
DocumentCode:

Abstract:
To improve individual GO term analysis algorithm for detecting differential gene expression, according to the directed acyclic graph structure property of gene classification system, Gene Ontology (GO), a novel and effective method named significant cluster analysis based on GO (ScaGO) was presented. The inputs of ScaGO were the expression values from a case-control microarrary experiment, aimed at detecting some novel differential expression changes. The results had shown some insights into gene expression difference at the functional level, towarded clarification of the process of pathological changes or mechanism of medicine. Both ScaGO and individual GO term analysis were applied to the acute lymphoblastic leukemia expression dataset and yeast Rap1 DNA-binding mutant dataset. Compared to individual GO term analysis, ScaGO was turned out to be more sensitive, and some novel differential expression changes which were mostly reported were mined successfully. It means that our ScaGO can provide the positive help in the experimental guidance. Fig 1, Tab 3, Ref 21

References

1 Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitor in of 1000 genes. Proc Natl Acad Sci U S A, 1996, 93 (20): 10614~10619
2 Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics, 2001, 17 (6): 509~519
3 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000, 25 (1): 25~29
4 Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R. A systems biology approach for pathway level analysis. Genome Res, 2007, 17 (10): 1537~1545
5 Trajkovski I, Lavrac N, Tolar J. SEGS: Search for enriched gene sets in microarray data. J Biomed Inform, 2008, 41 (4): 588~601
6 Nam D, Kim SB, Kim SK, Yang S, Kim SY, Chu IS. ADGO: Analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics, 2006, 22 (18): 2249~2253
7 Chiaretti S, Li X, Gentleman R, Vitale A, Wang KS, Mandelli F, Foa R, Ritz J. Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation. Clin Cancer Res, 2005, 11 (20): 7209~7219
8 Huber W, Heydebreck AV, Sueltmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 2002, 18: 96~104
9 Yarragudi A, Parfrey LW, Morse RH. Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res, 2007, 35 (1): 193~202
10 Resnik P. Using information content to evaluate semantic similarity in a taxonomy. Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal, Canada, 1995. 448~453
11 Jiang J, Conrath DJ. Semantic similarity based on corpus statistics and lexical taxonomy. Proceeding of International Conference Research on Computational Linguistics, Taipei, China, 1997. 19~33
12 Lin D. An information-theoretic definition of similarity. Proceedings of the 15th international conference on machine learning, Wisconsin, USA, 1998. 296~304
13 Kim SY, Volsky DJ. PAGE: Parametric analysis of gene set enrichment. BMC Bioinformatics, 2005, 6: 144
14 Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist, 2001, 29 (4): 1165~1188
15 Dierov J, Dierova R, Carroll M. BCR/ABL translocates to the nucleus and disrupts an ATR-dependent intra-S phase checkpoint. Cancer Cell, 2004, 5 (3): 275~285
16 Raitano AB, Halpern JR, Hambuch TM, Sawyers CL. The Bcr-Abl leukemia oncogene activates Jun kinase and requires Jun for transformation. Proc Natl Acad Sci USA, 1995, 92 (25): 11746~11750
17 Cambier N, Zhang Y, Vairo G, Kosmopoulos K, Metcalf D, Nicola NA, Elefanty AG. Expression of BCR-ABL in M1 myeloid leukemia cells induces differentiation without arresting proliferation. Oncogene, 1999, 18 (2): 343~352
18 Dupuy AG, L’Hoste S, Cherfils J, Camonis J, Gaudriault G, de Gunzburg J. Novel Rap1 dominant-negative mutants interfere selectively with C3G and Epac. Oncogene, 2005, 24 (28): 4509~4520
19 Scottt EW, Baker HV. Concerted action of the transcriptional activators REB1, RAP1, and GCR1 in the high-level expression of the glycolytic gene TPI. Mol Cell Biol, 1993, 13 (1): 543~550
20 Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E. Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet, 2003, 34 (3): 267~273
21 Hummel M, Meister R, Mansmann U. GlobalANCOVA: Exploration and assessment of gene group effects. Bioinformatics, 2008, 24 (1): 78~85

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Last Update: 2011-06-23