HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: 21/2/284    most recent 00236.2004v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Web of Science (12) Citing Articles via Google Scholar Google Scholar Articles by Chen, Z. Articles by Liu, L. Search for Related Content PubMed PubMed Citation Articles by Chen, Z. Articles by Liu, L.

Toolbox

RealSpot: software validating results from DNA microarray data analysis with spot images

Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma

The spot images from DNA microarray highly affect the discovery of biological knowledge from gene expression data. However, results from quality analysis, normalization, differential expression, and cluster analysis are rarely validated with spot images in current data analysis methods or software packages. We designed RealSpot, a software package, to validate the results by directly associating spot quality and data with spot images in a spreadsheet table. RealSpot splits hybridization images into individual spots stored in a spreadsheet table. It subsequently associates microarray data with spot images and performs data validation through the standard table operation such as sorting, searching, and editing. RealSpot has several built-in functions to facilitate data validation, including spot quality analysis, data organization, one-way ANOVA, gene ontology association, verification, import, and export. We used RealSpot to evaluate 77 slides (30,000 features each) from real hybridization experiments and to validate results from each step of data analysis. It took 10 min to validate results of spot quality after initial evaluation and correct 0.3% of falsely assigned qualities of 10,000 spots. We validated 1,641 of 2,110 differentially expressed genes identified by SAM analysis in 1/2 h by comparing each gene with its respective spot image. Furthermore, we found that 6 of 48 genes in one cluster from k-mean clustering method showed inconsistent trends of spot images. RealSpot is efficient for validating microarray results and thus helpful for improving the reliability of the whole microarray experiment for experimentalists.

spot quality; data normalization; data filtering

This article has been cited by other articles:

				M. Bhaskaran, Y. Wang, H. Zhang, T. Weng, P. Baviskar, Y. Guo, D. Gou, and L. Liu MicroRNA-127 modulates fetal lung development Physiol Genomics, May 13, 2009; 37(3): 268 - 278. [Abstract] [Full Text] [PDF]

				D. Gou, A. Mishra, T. Weng, L. Su, N. R. Chintagari, Z. Wang, H. Zhang, L. Gao, P. Wang, H. M. Stricker, et al. Annexin A2 Interactions with Rab14 in Alveolar Type II Cells J. Biol. Chem., May 9, 2008; 283(19): 13156 - 13164. [Abstract] [Full Text] [PDF]

				A. Daskalakis, D. Cavouras, P. Bougioukos, S. Kostopoulos, D. Glotsos, I. Kalatzis, G. C. Kagadis, C. Argyropoulos, and G. Nikiforidis Improving gene quantification by adjustable spot-image restoration Bioinformatics, September 1, 2007; 23(17): 2265 - 2272. [Abstract] [Full Text] [PDF]

				T. Weng, Z. Chen, N. Jin, L. Gao, and L. Liu Gene expression profiling identifies regulatory pathways involved in the late stage of rat fetal lung development Am J Physiol Lung Cell Mol Physiol, November 1, 2006; 291(5): L1027 - L1037. [Abstract] [Full Text] [PDF]

				J. Chen, Z. Chen, N. R. Chintagari, M. Bhaskaran, N. Jin, T. Narasaraju, and L. Liu Alveolar type I cells protect rat lung epithelium from oxidative injury J. Physiol., May 1, 2006; 572(3): 625 - 638. [Abstract] [Full Text] [PDF]

				M. Liang and B. Ventura Physiological genomics in PG and beyond: October to December 2005 Physiol Genomics, December 14, 2005; 24(1): 1 - 3. [Full Text] [PDF]