Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot
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Yvonne E Pittelkow
Visualisation methods for exploring microarray data are particularly important for gaining insight into data from gene expression experiments, such as those concerned with the development of an understanding of gene function and interactions. Further, good visualisation techniques are useful for outlier detection in microarray data and for aiding biological interpretation of results, as well as for presentation of overall summaries of the data. The biplot is particularly useful for the display of microarray data as both the genes and the chips can be simultaneously plotted. In this paper we describe several ordination techniques suitable for exploring microarray data, and we call these the GE-biplot, the Chip-plot and the Gene-plot. The general method is first evaluated on synthetic data simulated in accord with current biological interpretation of microarray data. Then it is applied to two well-known data sets, namely the colon data of Alon et al. (1999) and the leukaemia data of Golub et al. (1999). The usefulness of the approach for interpreting and comparing different analyses of the same data is demonstrated.
©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
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- Sampling Correction in Pedigree Analysis
- Parameter estimation for the calibration and variance stabilization of microarray data
- Transformations for cDNA Microarray Data
- Supervised Detection of Regulatory Motifs in DNA Sequences
- Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot
- On the Power of Profiles for Transcription Factor Binding Site Detection
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Artikel in diesem Heft
- Article
- Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants
- Sampling Correction in Pedigree Analysis
- Parameter estimation for the calibration and variance stabilization of microarray data
- Transformations for cDNA Microarray Data
- Supervised Detection of Regulatory Motifs in DNA Sequences
- Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot
- On the Power of Profiles for Transcription Factor Binding Site Detection
- An Empirical Bayesian Method for Differential Expression Studies Using One-Channel Microarray Data
