Article Figures & Data
Figures
- Figure 1.
Number of GeneChip Probe Sets Representing Genes That Were Either Upregulated or Downregulated at Various Times after Transfer of Plants from Warm (22°C) to Cold (4°C) Temperature.
- Figure 2.
Summary of Classes of Cold-Responsive Genes.
Details of selection criteria are described in the text. The total number of upregulated genes listed (218) is less than 156 (transient) + 64 (long-term) because probe sets representing two genes were present in both the transient and long term lists.
- Figure 3.
GeneChip Results for Genes Reported Previously as Upregulated during Cold Acclimation.
Probe sets used to calculate mean average difference values were as follows: COR47, probe sets 13225_s_at and 15997_s_at; ERD10, probe set 15103_s_at; COR78, probe set 15611_s_at; and COR6.6, probe sets 18699_i_at, 18700_r_at, and 18701_s_at. Where multiple probe sets were present that corresponded to a single gene, the mean average difference obtained for all corresponding probe sets was plotted.
- Figure 4.
Hierarchical Clustering of Cold-Responsive Genes.
The fold change values for genes that were upregulated (A) (n = 241 probe sets representing 218 genes) or downregulated (B) (n = 89 probe sets representing 88 genes) during cold acclimation (see Methods) were preprocessed so that fold change values that were associated with a difference call of no change were converted to 1. The mean of the four fold change values for each time point then was calculated, and the data were clustered using a Pearson correlation. Scales indicating the color assigned to each fold change are shown to the right of each cluster.
- Figure 5.
Hierarchical Clustering of Genes Upregulated by Cold.
Fold change values that were associated with a difference call of no change were converted to 1. The mean fold change values for each time point then were calculated, and the data were clustered. A scale indicating the color assigned to each fold change is shown to the right of the cluster.
(A) Clustering of the 64 genes (represented by 72 probe sets) that were upregulated by at least 2.5-fold after 7 days of cold treatment.
(B) Clustering of the 156 genes (represented by 169 probe sets) that were upregulated 3-fold at any time between 30 min and 24 h but were upregulated by less than 2.5-fold after 7 days of cold treatment.
- Figure 6.
“Binary” Hierarchical Clustering of Long-Term Upregulated Genes.
Data points at which the signal intensity indicated that the gene was present for both duplicate cold samples, that there was a difference call of increase for all four comparisons, and that the fold increase value was ≥2.5 for all four comparisons were assigned a value of 2 (red), whereas all other data points were assigned a value of 1 (black). The resulting data then were clustered. The probe set number and the description of the genes that fall into each cluster are indicated at right. The text color indicates the known or predicted role of each gene: metabolism, purple; cell growth, cell division, and DNA synthesis, light green; transcription, red; protein fate, gray; transport facilitation, light blue; intracellular transport, orange; cellular biogenesis, dark green; cellular communication and signal transduction, pink; cell rescue, defense, cell death, and aging, dark blue; unclassified proteins, black.
- Figure 8.
Hydropathy Plots for Novel COR-Like Proteins.
The amino acid sequence predicted from the sequence of COR-like proteins was analyzed using the method of Kyte and Doolittle (1982) to predict the regional hydropathy of the encoded polypeptides. Values > 0 correspond to hydrophilic regions, and values < 0 correspond to hydrophobic regions. The scale at top of each plot shows the number of amino acids from the N terminus of the polypeptide. The polypeptide encoded by At4g33550 is predicted to have a signal peptide (iPSORT; www.HypothesisCreator.net/iPSORT/) that is cleaved where indicated by the arrow. The hydropathy profile of COR6.6 is shown for comparison.
- Figure 9.
“Binary” Hierarchical Clustering of Transiently Upregulated Genes.
Data points at which the signal intensity indicated that the gene was present for both duplicate cold samples, that there was a difference call of increase for all four comparisons, and that the fold increase value was ≥3 for all four comparisons were assigned a value of 2 (red), whereas all other data points were assigned a value of 1 (black). The resulting data then were clustered. The probe set number and the description of the genes that fall into each cluster are indicated at right. The text color indicates the known or predicted role of each gene: metabolism, purple; cell growth, cell division, and DNA synthesis, light green; transcription, red; protein fate, gray; transport facilitation, light blue; intracellular transport, orange; cellular biogenesis, dark green; cellular communication and signal transduction, pink; cell rescue, defense, cell death, and aging, dark blue; unclassified proteins, black.
- Figure 10.
Venn Diagrams of Comparisons between Cold-Responsive Genes and Genes That Are Part of the CBF Regulon.
Sets of genes were selected using the criteria described in Methods. The number of genes in each set is displayed within a circle above a description of the set. Genes present in two sets are shown in the intersection of the two sets, so that the sum of the numbers within a circle is the total number of genes in that set.
(A) Intersection of genes that are upregulated in response to low temperature with those that are either upregulated by or independent of CBF overexpression.
(B) Intersection of genes that are either transiently or long-term upregulated in response to low temperature with those that are either upregulated by or independent of CBF overexpression.
(C) Intersection of genes that are downregulated in response to low temperature with those that are either downregulated by or independent of CBF overexpression.
- Figure 7.
Transcript Levels for Cold-Regulated Transcription Factors RAV1, ZAT12, and RAP2.1.
(A) Two-week-old wild-type (Wassilewskija-2) plants grown at 22°C were cold treated at 4°C, and tissue was harvested at the times indicated. Total RNA was isolated, and RNA gel blots were prepared (10 μg of RNA). The blots were hybridized with 32P-labeled probes for RAV1, ZAT12, and RAP2.1.
(B) Total RNA was isolated from 2-week-old plants from transgenic lines expressing the indicated CBF genes under the control of the 35S promoter of Cauliflower mosaic virus or carrying the empty vector (V). Total RNA was isolated from plants grown at warm temperature, and RNA gel blots were prepared (10 μg) and hybridized with a 32P-labeled probe for RAP2.1.
Additional Files
Data Supplement for THE PLANT CELL ONLINE: Volume 14, Issue 8 -- Page 1675
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