The table describes the annotation of 8145 clones in our collection. From those, 7385 clones was used on the array: 5655 cDNA clones from the Dictyostelium cDNA project (Morio, 1998; #13) (http://www.csm.biol.tsukuba.ac.jp/cDNAproject.html); 987 cDNA clones selected from a low redundancy screen of a lambda library (Shaulsky, 1995; #56) and a plasmid library (S. Lu and A. Kuspa, unpublished) of cDNA from late developmental stages, and from vegetative and early developmental stages of AX4 cells, respectively; 647 genomic DNA clones from the Dictyostelium Genome Project at Baylor College of Medicine (http://dictygenome.bcm.tmc.edu/) selected as long open reading frames that matched published protein sequences; and 96 clones from miscellaneous sources. All the clones were sequenced to verify their identity. Sequences were compared to public databases by a BLASTN and a BLASTX search against the NCBI database and against the Dictyostelium database (http://www.sdsc.edu/mpr/dicty/). Matching sequences were inspected manually by Bin Wang, Adam Kuspa and Gad Shaulsky, and the sequences that were considered as the most biologically significant were chosen as the annotating sequences. BLAST scores and P values are included in the table. The annotation includes the following prefixes: NSH, no significant homology; STN, similar to non-Dictyostelium gene; STD, similar to Dictyostelium gene. No prefix denotes that the clone is identical to a know Dictyostelium gene or that the sequence similarity is so high that the clone will report on the expression level of a known Dictyostelium gene.

Table 2. Data from Fig. 2B,C

This table contains the names and the data for the 2021 genes described in Fig. 2B,C as the consensus genes for Dictyostelium development. The columns 0 hr-24 hr are the means of the normalized log ratios from the four strain/nutrition experiments. The mean T and the median T are the mean and median T statistics of each array target against the contrast in each of the four experiments. The mean Var is the average of the by-target mean squared error in each of the four experiments. The pooled Var is the overall mean squared error of the target. P val 1 is the P value determined using a normal approximation for the mean T; P val 2 is the P value determined from the average P value of the T statistics from the four independent experiments; P val 3 is the Sidak multiple testing adjusted P value

 

Tables 3-6.

Data for all the 7385 targets on the array from the four strain/nutrition experiments. These data have been summarized to eliminate some of the redundant clones. The columns 0 hr-24 hr are the means of the normalized log ratios for each strain/nutrition experiment. The Var column is the mean squared error of each target, calculated using the targets residuals from the replicate arrays.

 

Table 7.

The average of the individual strain/nutrition experiments from Tables 3-6. It includes all the data used in the dissimilarity calculation that generated the dendogram in Fig. 2A. The data in Table 2 are derived from the data in this table. The columns 0 hr-24 hr are the means of the normalized log ratios from the four strain/nutrition experiments. The pooled Var is the overall mean squared error of each target.

 

Table 8-11.

The data for the cell-type enriched genes shown in Fig. 3A. The values in the first 12 columns are the normalized log ratios of individual array experiments. Cell type score is the T statistic of the array target against a particular linear contrast (the contrast coefficients are given in the normalization and analysis file). The time score is the linear contrast value against one of the two coefficient vectors. In Tables 8 and 11, the vector is (–1, 1.6, 1.6, 1.6, –1, –1, –1, –1, –1, –1, –1, 1.6, 1.6) and in Tables 9 and 10, the vector is determined by the line (y = x/12–1).

 

Table 12 is a summary of all the cell-type enrichment scores for all the targets in the array. The data in tables 8-11 are derived from the data in this table. The values in the first 4 columns are the by-cell type means of the normalized log ratios from the three replicate arrays. The Var is the mean squared error of each array target.

 

In all the tables, clone ID can be used to request materials by writing to Gad Shaulsky at gadi{at}bcm.tmc.edu.