Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)
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- Abstract
- Table of Contents
- Figures
- 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.
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PDF or HTML at Wiley Online LibraryTable 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
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PDF or HTML at Wiley Online LibraryFigures
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Figure 7.10.1 LAD front page. View Image -
Figure 7.10.2 LAD main menu. View Image -
Figure 7.10.3 Experiment file upload screen. View Image -
Figure 7.10.4 Experiment file upload results screen. View Image -
Figure 7.10.5 Experiment upload screen 1. View Image -
Figure 7.10.6 Experiment upload screen 2. View Image -
Figure 7.10.7 Experiment search screen. View Image -
Figure 7.10.8 Experiment search results screen. View Image -
Figure 7.10.9 Experiment search results screen from the original LAD server at the Iyer Lab, University of Texas, Austin. View Image -
Figure 7.10.10 Experiment editing screen. View Image -
Figure 7.10.11 Single experiment analysis icons. View Image -
Figure 7.10.12 Single experiment data filtering. View Image -
Figure 7.10.13 Single experiment data query results. View Image -
Figure 7.10.14 Single experiment data view screen. View Image -
Figure 7.10.15 Single experiment data distribution. View Image -
Figure 7.10.16 Single experiment plot data. View Image -
Figure 7.10.17 Plot produced via single experiment plot data screen (also see Fig. ). View Image -
Figure 7.10.18 Single experiment ratios on array (sample experiment). View Image -
Figure 7.10.19 Single experiment ratios on array with bias shown. View Image -
Figure 7.10.20 Single experiment channel intensities. View Image -
Figure 7.10.21 Select data grids (filters). View Image -
Figure 7.10.22 Data grids (results). View Image -
Figure 7.10.23 Gene annotation filters. View Image -
Figure 7.10.24 Raw data filters. View Image -
Figure 7.10.25 Final filters and data transformations. View Image -
Figure 7.10.26 Data extraction results. View Image -
Figure 7.10.27 “Save this dataset” screen. View Image -
Figure 7.10.28 Clustering and image generation—setup. View Image -
Figure 7.10.29 Clustering and image generation—generated. View Image -
Figure 7.10.30 Clustering and image generation—generated. View Image -
Figure 7.10.31 Array list creation. View Image -
Figure 7.10.32 Add experiment access by batch. View Image -
Figure 7.10.33 Experiment set creation. View Image -
Figure 7.10.34 Experiment set creation, part 2. View Image -
Figure 7.10.35 Publication creation. View Image -
Figure 7.10.36 LAD user registration page. View Image -
Figure 7.10.37 Login screen. View Image -
Figure 7.10.38 LAD main menu (curator). View Image -
Figure 7.10.39 Experiment group creation entry form. View Image -
Figure 7.10.40 LAD global resources links from the LAD main menu (also see Fig. ). View Image -
Figure 7.10.41 LAD print creation links from the LAD main menu (also see Fig. ). View Image -
Figure 7.10.42 Terminal display of LAD installation program. View Image -
Figure 7.10.43 Example /etc/crontab file with a suggested schedule. View Image
Videos
Literature Cited
| Literature Cited | |
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| 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. | |
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| 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., Volkert, T.L., Wilson, C.J., Bell, S.P., and Young, R.A. 2000. Genome‐wide location and function of DNA binding proteins. Science 290:2306‐2309. | |
| Sherlock, G., Hernandez‐Boussard, T., Kasarskis, A., Binkley, G., Matese, J.C., Dwight, S.S., Kaloper, M., Weng, S., Jin, H., Ball, C.A., Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D., and Cherry, J.M. 2001. The Stanford Microarray Database. Nucl. Acids Res. 29:152‐155. | |
| Yang, Y.H., Dudoit, S., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucl. Acids Res. 30:e15. |
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