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Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)

关键词： microarray data visualization来源：互联网

Abstract
Table of Contents
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Literature Cited

Abstract

The wide availability and use of DNA microarrays has brought the power of whole?genome functional characterization to a large variety of research environments. Microarrays, however, also introduce significant infrastructural and analytical concerns with respect to the long?term warehousing, annotation, and visualization of immense data sets. The Longhorn Array Database (LAD) is a MIAME?compliant microarray database that operates on PostgreSQL and Linux. It is a free and completely open?source software solution, and provides a systematic and proven environment in which vast experiment sets can be safely archived, securely accessed, biologically annotated, quantitatively analyzed, and visually explored. This unit provides the complete set of information needed to successfully deploy, configure, and use LAD for the purposes of two?color DNA microarray analysis and visualization.

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Table of Contents

Basic Protocol 1: Database Location and Authentication
Basic Protocol 2: Experiment Submission
Basic Protocol 3: Experiment Searching
Basic Protocol 4: Single‐Experiment Data Analysis
Basic Protocol 5: Multiexperiment Data Analysis
Support Protocol 1: Synthetically Generate Multiple Experiments for
Basic Protocol 6: Manipulating Stored Datasets and Exportable Files
Basic Protocol 7: Creating Array Lists
Basic Protocol 8: Open Data Publication
Guidelines for Understanding Results
Commentary
Appendix A: User Account Creation
Appendix B: Global Resource Creation and Management
Appendix C: Installation of the Longhorn Array Database
Literature Cited
Figures
Tables

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Materials

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Figures

Figure 7.10.1 LAD front page.

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Figure 7.10.2 LAD main menu.

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Figure 7.10.3 Experiment file upload screen.

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Figure 7.10.4 Experiment file upload results screen.

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Figure 7.10.5 Experiment upload screen 1.

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Figure 7.10.6 Experiment upload screen 2.

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Figure 7.10.7 Experiment search screen.

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Figure 7.10.8 Experiment search results screen.

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Figure 7.10.9 Experiment search results screen from the original LAD server at the Iyer Lab, University of Texas, Austin.

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Figure 7.10.10 Experiment editing screen.

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Figure 7.10.11 Single experiment analysis icons.

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Figure 7.10.12 Single experiment data filtering.

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Figure 7.10.13 Single experiment data query results.

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Figure 7.10.14 Single experiment data view screen.

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Figure 7.10.15 Single experiment data distribution.

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Figure 7.10.16 Single experiment plot data.

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Figure 7.10.17 Plot produced via single experiment plot data screen (also see Fig. ).

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Figure 7.10.18 Single experiment ratios on array (sample experiment).

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Figure 7.10.19 Single experiment ratios on array with bias shown.

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Figure 7.10.20 Single experiment channel intensities.

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Figure 7.10.21 Select data grids (filters).

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Figure 7.10.22 Data grids (results).

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Figure 7.10.23 Gene annotation filters.

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Figure 7.10.24 Raw data filters.

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Figure 7.10.25 Final filters and data transformations.

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Figure 7.10.26 Data extraction results.

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Figure 7.10.27 “Save this dataset” screen.

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Figure 7.10.28 Clustering and image generation—setup.

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Figure 7.10.29 Clustering and image generation—generated.

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Figure 7.10.30 Clustering and image generation—generated.

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Figure 7.10.31 Array list creation.

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Figure 7.10.32 Add experiment access by batch.

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Figure 7.10.33 Experiment set creation.

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Figure 7.10.34 Experiment set creation, part 2.

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Figure 7.10.35 Publication creation.

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Figure 7.10.36 LAD user registration page.

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Figure 7.10.37 Login screen.

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Figure 7.10.38 LAD main menu (curator).

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Figure 7.10.39 Experiment group creation entry form.

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Figure 7.10.40 LAD global resources links from the LAD main menu (also see Fig. ).

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Figure 7.10.41 LAD print creation links from the LAD main menu (also see Fig. ).

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Figure 7.10.42 Terminal display of LAD installation program.

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Figure 7.10.43 Example /etc/crontab file with a suggested schedule.

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Videos

Literature Cited

Literature Cited
	Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze‐Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. 2001. Minimum information about a microarray experiment (MIAME): Toward standards for microarray data. Nat. Genet. 29:365‐371.
	Cherry, J.M., Adler, C., Ball, C., Chervitz, S.A., Dwight, S.S., Hester, E.T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. 1998. SGD: Saccharomyces Genome Database. Nucl. Acids Res. 26:73‐79.
	Dudoit, S., Gentleman, R.C., and Quackenbush, J. 2003. Open source software for the analysis of microarray data. BioTechniques Suppl:45‐51.
	Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome‐wide expression patterns. Proc. Natl. Acad. Sci. U.S.A 95:14863‐14868.
	Hahn, J.S., Hu, Z., Thiele, D.J., and Iyer, V.R. 2004. Genome‐wide analysis of the biology of stress responses through heat shock transcription factor. Mol. Cell. Biol. 24:5249‐5256.
	Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell‐cycle transcription factors SBF and MBF. Nature 409:533‐538.
	Kerr, M.K., Martin, M., and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7:819‐837.
	Killion, P.J., Sherlock, G., and Iyer, V.R. 2003. The Longhorn Array Database (LAD): An open‐source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics 4:32.
	Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volk

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