The following additional data are available with the online version of this paper. Additional data file 1 lists enriched genes from the larval pan-neural (LP), embryonic pan-neural (EP), larval A-class (LA), and embryonic A-class (EA) microarray datasets. Additional data file 2 is a master annotation file of all spots on the C. elegans Affymetrix microarray (based on WormBase releases WS140 and WS146). Additional data file 3 is a master annotation file of all genes represented on the C. elegans Affymetrix microarray (based on WormBase releases WS140 and WS146). Additional data file 4 lists LP, EP, LA, and EA enriched datasets categorized into gene families. Additional data file 5 is a comparison of the LP and LA enriched transcripts to the 1,926 GMI enriched genes found on the C. elegans Affymetrix chip [13]. Additional data file 6 lists the 50 top-ranked muscle enriched genes (RMF, DMM, unpublished data). Additional data file 7 lists LP enriched genes with known expression patterns from Figure 3b. Additional data file 8 includes representative scatter plots and R2 values for pairwise combinations of the EP and LA datasets. Additional data file 9 lists 27 uncharacterized human homologues in the LP and EP datasets, and indicates mouse homolog and expression in mouse brain. Additional data file 10 shows provides comparisons of all enriched datasets (LP versus EP; LP versus LA; EP versus EA; LA versus EA) shown in Figure 8. Additional data file 11 provides comparisons of all enriched datasets versus a MAPCeL profile of chemosensory neurons (AFD/AWB) [8] shown in Figure 8. Additional data file 12 lists EGs from the embryonic EP, EA, and embryonic reference (ER) datasets. Additional data file 13 lists EGs from the LP, LA, and larval reference (LR) datasets. Additional data file 14 list 11,868 unique transcripts identified by all of our microarray experiments. Additional data file 15 provides a comparison of the GMIc dataset to the LP EG and LR EG datasets. Additional data file 16 lists the approximately 1,600 EGs without EST confirmation plus a subset enriched in the LP, EP, EA, and LA neural datasets.
Additional data file 17 is a complete list of GFP expression patterns. Additional data file 18 is a description of the dauer pathway genes identified in our LP and EP enriched datasets. Additional data file 19 lists the 162 common A-class enriched genes categorized into gene families. Additional data file 20 provides the mRNA-tagging bench protocol. Additional data file 21 lists the genes identified by MAS5.0 as present in at least two-thirds of LP replicates and three-quarters of LA replicates. The RMA normalized intensity values for these genes, plus those from the LR dataset, are included. Additional data file 22 is a Perl script used to search WormBase expression data (keyword_search.pl). Additional data file 23 list the keywords used to search WormBase expression data. Additional data file 24 lists enriched genes from all datasets (LP, EP, LA, EA) with uncharacterized human homologues. Additional data file 25 lists the MAS5.0 intensities for the EP, LP, and LA datasets. Additional data file 26 lists the MAS5.0 intensities for the LR dataset. Additional data file 27 lists the RMA intensities for the LP, LA, and LR datasets. Additional data file 28 lists the RMA intensities for the EP and ER datasets. Additional data file 29 is a comparison of the EP and LP enriched datasets to the list of candidate neural genes containing a presumptive pan-neural cis-regulatory element [48].
Answers to all your Biology Questions
