Online Supplement for Wieczorek et al. (2006)
These pages contain supplementary material for the manuscript.
Expansins are involved in the formation of nematode-induced
syncytia in roots of Arabidopsis thaliana
Krzysztof Wieczorek,1
Bettina Golecki,2, a
Lars Gerdes,2, b
Petra Heinen,1
Dagmar Szakasits,1
Daniel M. Durachko,3
Daniel J. Cosgrove,3
David P. Kreil,4
Piotr S. Puzio,2, c
Holger Bohlmann,1
Florian M. W. Grundler1
- Institute of Plant Protection, Department of Applied Plant
Sciences and Plant Biotechnology, University of Natural Resources and
Applied Life Sciences, Vienna, Austria
- Institut für Phytopathologie, Christian-Albrechts-Universität
Kiel, Germany
- Department of Biology, 208 Mueller Lab, Pennsylvania State
University, University Park, Pennsylvania, 16870 USA
- Chair of Bioinformatics, Department of Biotechnology, University
of Natural Resources and Applied Life Sciences, Vienna, Austria
Current addresses:
a ALW Kiel, Germany;
b Institute of Botany, Ludwig-Maximilian-University Munich,
Germany;
c Metanomics GmbH, Berlin, Germany
See main manuscript for method references (subscription required).
Diagnostic plots, Q/A, Normalization
Diagnostic plots are provided of the raw, unnormalized data. These
have been used to determine an appropriate normalization method.
- Traditional M(A) plots for all pairs of chips showing the need for
normalization after probe sequence specific background
subtraction. Some summary statistics are included in panels below the
diagonal. Coloured curves track a loess fit of M(A).
[ 3.2MB pdf ]
- Exploratory scatter plots (panels above diagonal) and
quantile-quantile plots (panels below diagonal), both after probe
sequence specific background subtraction. The lack of systematic
trends in the quantile-quantile plots mapping to biological classes
indicates the suitability of quantile-quantile normalization for this
data set.
[ 4.7MB pdf ]
- M(A) plots as above, after quantile-quantile normalization.
[ 3.2MB pdf ]
- Scatter plots and quantile-quantile plots as above, after
quantile-quantile normalization.
[ 4.7MB pdf ]
- Residuals in a robust fit of a linear probe level model after
probe sequence specific background subtraction and quantile-quantile
normalization. These show spatial artefacts, which are dealt with by
appropriate downweighting of the affected probes in a robust iterative
weighted least squares fit in the probe signal summarization
process.
[ 23.6MB pdf ]
Results
After normalization of the entire data set, analysis was restricted to
known expansins for increased power of statistical tests.
- Normalized expansin transcript signals on log2
scale.
[ 3.6KB txt ]
- Pairwise contrasts in a batch detrending linear model.
[ 26.5KB xls | 6.6KB pdf ]