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Global Analysis of Gene Expression in the Dauer Larvae of Caenorhabditis elegans

John Wang 1 and Stuart K. Kim1,2,3


1Department of Developmental Biology
Stanford University Medical Center
Stanford, CA 94305

2Department of Genetics
Stanford University Medical Center
Stanford, CA 94305

3corresponding author
650-725-7671
650-725-7739
kim@cmgm.stanford.edu

Chip and SOM picture


 

SUPPLEMENTAL INFORMATION

Supplemental Tables

  • S-Table 1  Full averaged data. The average log2 expression value relative to the 0 hour for the dauer exit and L1 starvation time courses for all the genes. This table also contains the magnitude of difference between the minimum and maximum expression levels during the dauer exit and L1 feeding time courses. To analyze the time course data using magnitude of expression change, first download this table and sort by the preferred threshold. The difference between T0 and T12 in the dauer adjustment experiment is also included.  [text 5.6M]  Caution large file

     

  • S-Table 2  All Raw data. This table contains the original normalized log2(expt/ref) expression ratio data downloaded from the Stanford Microarray Database for each gene. Additionally, this tables includes the p-values that were calculated for the Student's t-test, 1-way ANOVA and 2-way mixed-model ANOVA comparisons for each gene.  [text 13.7M]  Caution large file

     

  • S-Table 3 List of 2430 genes that pass 1-way ANOVA p<0.001  [text]

     

  • S-Table 4 List of 1984 genes that pass 2-way mixed model ANOVA p<0.05  [text]
         NEW!
    • [text]   List of Transient Genes
    • [text]   List of Early Genes
    • [text]   List of Climbing Genes
    • [text]   List of Late Genes
    • [text]   List of Dauer Enriched Genes

     

  • S-Table 5 List of 446 genes that are common to feeding 2-way mixed model ANOVA p>0.05  [text]

     

  • S-Table 6 List of 220 genes that were removed because of contamination  [text]

     

  • S-Table 7 List of my lists  [text]
    Gene annotations are constantly changing, so the numbers and members of each gene category described in this supplemental data website reflect that prior to or at the time of the writing of this paper.
    We have discovered one minor discrepancy in the gene lists presented in Tables 1 and 2. The “Translation Factors” gene list is based on annotation by Proteome and Table 1 [May 2002] is more up-to-date than Table 2 [Oct 2000]. The difference is that Table 1 has 4 genes added to and 2 genes removed from the older Table 2 list. The number of overlapping genes in Table 2A between the “Translation factors” gene group and the “early” gene class is still six and the hypergeometric probability is still significant (p<0.001). The four genes added to the Table 1 version are F53A2.6, B0348.6, Y57A10A.EE and unc-37 (W02D3.9); the two genes removed are C43E11.4 and T05G5.10. The full list of genes for both version are in Supplemental S-Table 7.

     


  • Comparison to SAGE data from Jones et al. 2001

    CLICK THUMBNAIL
    to explore SAGE data on
    dauer exit and L1 starvation dataset.

    SAGE Cluster
  • SAGE genes with microarray data List of 305 SAGE genes in the dataset lists.  [text]

     

  • Dauer ratios for the 305 SAGE genes List of 305 SAGE genes in the dataset lists.  [text]

     


  • Additional expression profiles for mountains 5 and 22

    S-Figure 1 Enlarged figure of mount 5

    or
    CLICK THUMBNAIL to explore mount 5 data on
    dauer exit and L1 starvation dataset.

    Mount 5 Cluster


    S-Figure 2 Enlarged figure of mount 22

    or
    CLICK THUMBNAIL to explore mount 22 data on
    dauer exit and L1 starvation dataset.

    Mount 22 Cluster

    Additional expression profiles for hh-like genes
    warthogs, groundhogs, ground-like

    S-Figure 3 Enlarged figure of hh-like genes

    or
    CLICK THUMBNAIL to explore data for hh-like genes on
    dauer exit and L1 starvation dataset.

    hh-like genes Cluster

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     Last updated June 24, 2004