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Open Access Research article

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem

Hardy Hall12 and Brian Ellis1*

Author Affiliations

1 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

2 Currently: Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden

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BMC Plant Biology 2013, 13:14  doi:10.1186/1471-2229-13-14

Published: 25 January 2013

Additional files

Additional file 1: Figure S1:

Surface plots of relative elongation growth rates and LOWESS-predicted growth kinematic profiles (n=34). Plotting as described in Hall & Ellis (2012) except that segments are numbered from bottom upwards for surface plots. Plants arranged by column according to independently grown and observed batches.

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Additional file 2: Table S1 part 1:

Raw, processed data, TAIR10 annotations and clustering information for all gene-specific array elements. See first tab of file for column header descriptions.

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Additional file 3: Table S1 part 2:

Raw, processed data, TAIR10 annotations and clustering information for all gene-specific array elements. See first tab of file for column header descriptions.

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Additional file 4: Table S1 part 3:

Raw, processed data, TAIR10 annotations and clustering information for all gene-specific array elements. See first tab of file for column header descriptions.

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Additional file 5: Table S2:

ATCOECIS reports for enrichment of gene ontology (GO) terms for genes most significantly different (q-value<4.7E-02) between YNG and MGR stages. GO terms appearing more than once in the gene list are shown ranked according to significance of enrichment p-value (<0.05). Only GO terms with two or more genes in the input set and showing enrichment compared to the background frequency (in the full genome) are reported (number of genes indicated in brackets). Score indicates the fraction of input genes annotated with the GO term. 'Term occurrences' column indicates the number of co-occurrences of each GO term in the AtCoeCis results among all expression categories (left-most column).

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Additional file 6: Table S3:

ATCOECIS reports for enrichment of gene ontology (GO) terms for genes most significantly different (q-value<6.72E-02) between MGR and CSS stages. GO terms appearing more than once in the gene list are shown ranked according to significance of enrichment p-value (<0.05). Only GO terms with two or more genes in the input set and showing enrichment compared to the background frequency (in the full genome) are reported (number of genes indicated in brackets).[move to methods; P-values are calculated using the hypergeometric distribution [17]. Score indicates the fraction of input genes annotated with the GO term. 'Term occurrences' column indicates the number of co-occurences of each GO term in the AtCoeCis results among all expression categories (left-most column).

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Additional file 7: Table S4:

ATCOECIS reports for enrichment of gene ontology (GO) terms for genes most significantly different (q-value<4.9E-02) between CSS and OLD stages. GO terms appearing more than once in the gene list are shown ranked according to significance of enrichment p-value (<0.3). Only GO terms with two or more genes in the input set and showing enrichment compared to the background frequency (in the full genome) are reported (number of genes indicated in brackets). Score indicates the fraction of input genes annotated with the GO term. 'Term occurrences' column indicates the number of co-occurences of each GO term in the AtCoeCis results among all expression categories (left-most column).

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Additional file 8: Table S5:

List of Arabidopsis gene index (AGI) codes for each of the genes in the clusters specified in Figure 2.

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Additional file 9: Figure S2:

Boxplots depicting distribution of estimates of relative gene expression (fold-change) of each developmental stage for the sub-clusters identified in Figure 2. Boxes bound upper and lower quartiles, dark horizontal bars denote median values, whiskers represent 95% confidence intervals, circles represent outliers occuring in upper and lower 2.5 percentiles. Cluster 8 is also depicted in Figure 2.

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Additional file 10: Figure S3:

Gene ontology (GO) SLIM term enrichment analysis for clusters depicted in Figure 2. A) Boxplots depicting distribution of term enrichment across all clusters, expressed as fold-change relative to abundance in the full genome, for each of the three GO SLIM categories; 'cellular component', 'molecular function', and 'biological process'. Boxes bound upper and lower quartiles, dark horizontal bars denote median values, whiskers represent 95% confidence intervals, circles represent outliers occuring in upper and lower 2.5 percentiles. B) Barplots exhibiting term enrichment for each cluster in each of the three GO SLIM categories; colour assignment for bars is indicated in Figure 'A'. The number of genes (accessions) included in each cluster is indicated at the base of the 'biological process' barplot.

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Additional file 11: Table S6:

ATCOECIS reports for enrichment of gene ontology (GO) terms for [sub] clusters of genes displaying stage-specific expression. Top 10 most significant over-represented GO terms appearing more than once in the gene list are shown ranked according to p-value (<0.05). Only GO terms with two or more genes in the input set and showing enrichment compared to the background frequency (in the full genome) are reported (number of genes indicated in brackets). Score indicates the fraction of input genes annotated with the GO term. 'Term occurrences' column indicates the number of co-occurrences of each GO term in the AtCoeCis results among all expression categories (left-most column).

Format: XLSX Size: 45KB Download file

Open Data