"... In PAGE 60: ... Figure 55 also shows that the signal is reproducible. The time from one stabile level to another is about the same as for the temperature under the flow cell (Figure 53 and Table6 ). It takes the signal 3 min.... ..."

"... In PAGE 5: ... tern) for partitioning data into correlated sets. The number of partitions, along with the number of samples in each par- tition is illustrated in Table1 . For example, dataset alpha is partitioned into 13 groups, with groups containing 200, 46, .... ..."

"... In PAGE 5: ...sented in the microarray:stigma:ovary ratios at gt;100:1, and 16 at gt;10:1. In addition, of the 30 stigma messages that were most enriched relative to ovary messages in the microarray experiment, 22 were recovered in the sub- tracted stigma cDNA library ( Table2 ). Taken together, these data indicate that cDNA subtraction screening provides a powerful approach that can independently confirm large datasets generated in a microarray expression profile.... In PAGE 5: ... Eight genes that were implicated on the microarrays as being expressed at 20 to 300-fold higher levels in stigmas compared to ovaries were not represented by the se- quences obtained from the cDNA library. These genes are likely represented at a reduced level in the cDNA library due to their lower absolute levels of expression ( Table2 ). In addition, not all messages recovered in the cDNA library were preferentially expressed in the stig- ma, presumably due to incomplete subtraction.... ..."

"... In PAGE 2: ... Genes that were induced in at least four of the five experiments and were overexpressed by an average factor of two or more over the five experiments compared with the normal non-HS worms were identified (Table 1). DNA Motifs Identified from Promoters of HS Genes Because some amount of noise is frequently observed in DNA microarray experiments, we considered only those genes up- regulated by an average factor of four or more ( Table1 ) for the purpose of transcription regulatory element identification. Genes F44E5.... In PAGE 9: ... We therefore compiled the data from the five experiments to generate a list of genes that showed reproducible HS induc- tion independent of genotype or HS regime (Table 1). Identification of DNA Motifs Two DNA pattern recognition programs, ANN-Spec (Work- man and Stormo 2000) and Consensus (Hertz and Stormo 1999), were used to identify significant DNA patterns from the promoter regions (H11502500 to H115021 relative to the translation start) of the HS genes up-regulated by an average factor of four or more over the five cDNA experiments ( Table1 ). Consen- sus and ANN-Spec are local multiple sequence alignment programs that run on a given set of sequences (training set) to identify conserved motifs commonly present in those se- quences.... ..."

"... In PAGE 3: ... Genes that were induced in at least four of the five experiments and were overexpressed by an average factor of two or more over the five experiments compared with the normal non-HS worms were identified (Table 1). DNA Motifs Identified from Promoters of HS Genes Because some amount of noise is frequently observed in DNA microarray experiments, we considered only those genes up- regulated by an average factor of four or more ( Table1 ) for the purpose of transcription regulatory element identification. Genes F44E5.... In PAGE 10: ... We therefore compiled the data from the five experiments to generate a list of genes that showed reproducible HS induc- tion independent of genotype or HS regime (Table 1). Identification of DNA Motifs Two DNA pattern recognition programs, ANN-Spec (Work- man and Stormo 2000) and Consensus (Hertz and Stormo 1999), were used to identify significant DNA patterns from the promoter regions (H11502500 to H115021 relative to the translation start) of the HS genes up-regulated by an average factor of four or more over the five cDNA experiments ( Table1 ). Consen- sus and ANN-Spec are local multiple sequence alignment programs that run on a given set of sequences (training set) to identify conserved motifs commonly present in those se- quences.... ..."

"... In PAGE 5: ... 259 upregulated genes passed this filter for the experiment in the absence of CHX whereas 131 genes passed this filter for the experiment with CHX; 38 genes were found to be common to these two groups (see the Venn diagram in Fig. 2A and Table1... In PAGE 7: ... In order to analyze genes regulated by CHX in the absence of p53, H1299 cells were incubated at 32o in the presence of CHX and RNA was collected at 2h and 6h and analyzed by hybridization to the DNA microarray. Three genes from the 38 primary upregulated genes ( Table1 ) were also upregulated by CHX alone. These are the ATF3 (activated transcription factor 3), Histone 2A like protein and Bak.... In PAGE 14: ... This type of heterogeneity of expression indicates that not all p53-targets are activated in all conditions and a similar conclusion was pointed out also by other studies (Yu et al 1999, Zhao et al 2000). We also tried to analyze for the presence of p53 consensus targets in several of the genes listed in Table1 . This was performed by searching for the sequence of the two consensus decamers RRRCWWGYYY, separated by a gap of 0-13 nucleotides, in the sequence which is 2kbp upstream and downstream to the RNA start.... In PAGE 15: ...enes in various cells lines as was pointed out previously (Zhao et al., 2000; Yu et al., 1999). For example, in H1299 cells we found activation of several genes known to be involved in neuronal growth ( Table1 ) which may be unique to this cell type. Several reasons may account for the heterogeneity of p53 target genes.... In PAGE 24: ... (A) The dendrogram of the genes that include clusters of size 4 and larger. Each cluster is represented by a box colored according to the percent of primary target genes (38 genes, see Table1 ) contained in the cluster. The distribution of the 38 ... In PAGE 25: ... The cluster marked by an arrow (c) contains 87% of the 38 primary genes. The cluster marked by b contains all the 38 primary genes and the cluster marked by a contains the 9 genes that show different kinetics ( Table1 and Fig. 4) Fig.... In PAGE 31: ...31 Table Legend: Table1 . Primary target genes upregulated by p53.... ..."