Supplemental web site for Transcriptional Profile of Aging in C. Elegans

James Lund1, Patricia Tedesco2, Kyle Duke 1, Stuart K. Kim1, Chris Link2 and Thomas E. Johnson2,3

1Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, CA 94305.
2Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309
3 Corresponding author


The manuscript in PDF format.


Search and graph gene expression profiles


 

Figure 1

Expression profile of 164 aging-regulated genes. Each column shows the average of log2(experiment/reference), normalized to expression at day 3. Scale shows level of expression. Genes were hierarchically clustered based on Pearson correlation coefficients.

Aging regulated genes

Click on image to view genes.

PDF version of figure 1.

Supplemental Figure 1, maturity genes


Figure 2.

Aging profiles for specific classes of genes. The average of the log2(expression ratio) for each gene relative to day 3 is shown. Genes were hierarchically clustered based on Pearson correlation coefficients. Scale shows expression level. a. Insulin-related genes. Bold indicates four insulin-like genes that change expression levels during aging (p < .05). b. Homologs of the yeast sir-2 gene. c. Genes that encode heat shock proteins. d. Average expression of Tc3 and Mariner genes. For each transposon element copy, the average log2(expression ratio) was calculated from the microarray hybridization repeats, and then the average from all copies of each transposon was calculated (since each copy has nearly identical sequence and will cross-hybridize). Data for each of the individual transposable elements are shown in supplemental figure 2.

Click on images to view genes.

Fig. 2a. Insulin-related genes.
Fig. 2b. Homologs of the yeast sir-2 gene.
Fig. 2c. Heat shock proteins.
Fig. 2d. Tc3 and Mariner genes.

PDF version of figure 2.

(tab-delimited text) Supplemental Table 4. Tc3 transposon data.

(tab-delimited text) Supplemental Table 5. Mariner transposon data.


Figure 3.

Expression profile of muscle, neuronal, germ line-intrinsic and oocyte genes. Each row corresponds to a different gene. Gene identities and their expression are shown in Figure 3 at the supplemental web site. Scale shows expression ratio. a. 46 genes previously known to be expressed specifically in muscle. b. 88 neuronal-specific genes. c. 508 germ line-intrinsic genes expressed in both sperm-producing and oocyte-producing animals. D. 250 oocyte-enriched genes.

Click on images to view genes.

Fig. 3a. Muscle genes.
Fig. 3b. Neuronal-specific genes.
Fig. 3c. Germ line-intrinsic genes.
Fig. 3d. Oocyte-enriched genes.

PDF version of figure 3.


Figure 4.

Expression profile of genes in mount 15 during aging and dauer exit. Each row corresponds a gene from mount 15, which is one of the gene clusters from the gene expression topomap. First six columns shows expression ratios in the aging time course. Last column shows expression ratio of non-dauer/dauer samples. Scale shows level of expression.

Fig. 4. Click on image to view genes.

PDF version of figure 4.


Supplemental Table 1.

Supplemental Table 2.

Supplemental Table 3.


Supplemental Figure 2, examination of strain differences.


Please send comments or questions regarding this web site to Jim Lund (jiml@stanford.edu).