Online Supplement for Szakasits et al. (2008)
These pages contain supplementary material for the manuscript.
The Transcriptome of Syncytia Induced by the Cyst Nematode
Heterodera schachtii in Arabidopsis Roots
David P. Kreil,3
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
- RZPD, Germany; present address: ATLAS Biolabs GmbH,
- WWTF Chair of Bioinformatics, Department of Biotechnology, University
of Natural Resources and Applied Life Sciences, Vienna, Austria
Add link to original journal article once published.
These pages provide a comprehensive archive of supplementary data and
results for the above journal manuscript. The tables comprise
thousands of pages and are provided so that readers can easily search
for particular genes in the list of results.
This page lists content sorted by type and in the context of a short
description. To complement this, for easier reference by figure and
table number (following the order of appearance in the manuscript
text), please use the below links:
Appendix S1: Methods
We provide supplementary documents providing
further details on the microarray experiments and data analysis methods
employed as well as particulars about the performed
quantitative real-time and in situ
Appendix S2: Archive of data and sample description tables
An archive containing the raw CEL data for the 11 hybridizations
analysed in the paper will be made available here from
the publication date.
[ 37.3MB zip ]
We provide an extensive description of the performed sample
measurements through a table of target meta
data (one row per sample).
- After normalization and weighted summarization using
reannotated probesets as detailed in the Methods section we obtained
the normalized transcript signals on log2-equivalent scale
underlying subsequent statistical analysis.
[ 3.3MB zip ]
Appendix S3: Low-level microarray analysis and diagnostic plots
Diagnostic plots are provided of the raw, unnormalized data. These
have been used to determine an appropriate normalization
method. Subsequent diagnostics verify successful normalization and
examine data set characteristics for systematic trends and artefacts.
- 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).
[ 8.1MB 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
[ 11.2MB pdf ]
- Residuals in a robust fit of a linear probe level model after
probe sequence specific background subtraction and quantile-quantile
normalization. These show some random spatial artefacts, which have
been dealt with by appropriate downweighting of the affected probes in
a robust iterative weighted least squares fit in the probe signal
[ 23.9MB pdf ]
- Main contrasts in a batch detrending linear model are listed in the comprehensive tables below.
[Supplementary Table 1] Contrast: Syncytium vs Root. Listing differential expression for all genes.
[ 5.0MB pdf ]
Subsets of this table showing differential expression for a
multiple-testing corrected FDR<5% are available as
Supplementary Table 2 (upregulation) and
Supplementary Table 3 (downregulation).
[Supplementary Table 7] Contrast: 15 dpi Syncytium vs
5 dpi Syncytium. Listing differential expression for all genes.
[ 4.3MB pdf ]
A subset of this table showing differential expression for a
multiple-testing corrected FDR<5% is available as
Supplementary Table 6, showing (a) upregulated and
(b) downregulated genes.
[Supplementary Table 5] The 10% most highly expressed genes in Syncytia.
[ 490kB pdf ]
- [Supplementary Table 4] Contingency Tables for Fisher's
(a) Contingency tables and Fisher's Exact test for the
overrepresentation of peroxidase
genes in downregulated transcripts.
(b) Contingency tables and Fisher's Exact test for the
overrepresentation of MIPS genes in
- [Supplementary Table 8] Gene Ontology Analysis
(a) GO categories
(b) GO categories
Tables are tab-delimited and are easily viewed in all popular
- [Supplementary Table 9] Genevestigator
table. Expression of the 100 strongest upregulated genes according
- M(A) plots for main contrasts including standard
errors (grey bars).
[Supplementary Figure 1] Contrast: Syncytium vs Root.
See Table S1 for a full list of gene names
(5.0 MB pdf).
[ 824kB pdf ]
[Supplementary Figure 2] Contrast: 15 dpi Syncytium vs 5 dpi Syncytium.
[ 814kB pdf ]