BodyMap: a collection of 3' ESTs for analysis of human gene expression information

Abstract

BodyMap is a collection of site-directed 3' expressed sequence tags (ESTs) (gene signatures, GSs) that contains the transcript compositions of various human tissues and was the first systematic effort to acquire gene expression data. For the construction of BodyMap, cDNA libraries were made, preserving abundance information and histologic resolutions of tissue mRNAs. By sequencing 164,000 randomly selected clones, 88,587 GSs that represent chromosomally coded transcripts have been collected from 51 human organs and tissues. They were clustered into 18,722 independent 3' termini from transcripts, and more than 3000 of these were not found among ESTs assembled in UniGene (Build 75). Assessment of the prevalence of polyadenylation signals and comparison with GenBank cDNAs indicated that there was no significant contamination by internally primed cDNAs or genomic fragments but that there was a relatively high incidence (12%) of alternative polyadenylation sites. We evaluated the sensitivity and resolution of expression information in BodyMap by in silico Northern hybridization and selection of tissue-specific gene probes. BodyMap is a unique resource for estimation of the absolute abundance of transcripts and selection of gene probes for efficient hybridization-based gene expression profiling.

Figure 1

Distribution of AATAAA and single-base variants in 3′ ends of ESTs. (A) The hexanucleotide signals from the 3′ ends of four sets of cDNA sequences. The regions 10–50 bp from the polyadenylation sites were examined for the presence of AATAAA or its single-base variants. The 3′ ESTs from dbEST were divided into those starting with more than seven Ts (Tn > 7) and those without a T in the first position (T₀). (B) The prevalence of each single-base variant in the cDNA termini with only one variant signal and no AATAAA within the 10–50-bp region from the poly(A) tail in each of four data sets is shown. The frequencies (%) of all 18 possible variants in each data set are shown beside bars. In vitro polyadenylation activities for each variant measured in the context of the SV40 polyadenylation signal are reproduced from the literature (Wickens et al. 1984; Sheets et al. 1990)

Figure 2

The relative contents of the most abundant transcripts in 51 human tissues or cell types as measured by gene signature collection. The error range indicates the P value of 0.1 calculated for each observed occurrence. The identities of some transcripts are given. For the identities of other transcripts, see Table 1.

Figure 3

Cumulative frequencies of gene signature (GS) sequences. The cumulative sums calculated in descending order of GS frequencies are plotted as a percentage of total tag occurrence. Tag occurrences in each of three major tissue categories were plotted separately.