During the assembly o UniGene [19], we retained the library source for each EST, via links provided by UniGene to the IMAGE consortium [37]. Most of the 2,500 libraries comprising UniGene ESTs were derived from single tissues or embryonic stages, and we further standardized the library source annotation into 102 categories. Keywords and derived categories are available as additional data files. The most highly represented categories were various types of tumors (15.0% of all ESTs), fetal tissue (10.7%), embryo (6.2%), infant (5.1%), and testis (4.3%). We reasoned that some genes might exhibit highly tissue-specific expression, such that most of the ESTs comprising a transcript would be derived from the tissue. The identified genes are potential candidates for diseases of the involved tissues. Similar approaches have been used to identify candidate genes for pathologies of the prostate [38] and retina [39]. We explore here the global nature of tissue/source specificity. The result was 7,459 HINT transcripts with highly significant tissue-specificity (11%). Many of these are known genes, and an examination of the most specific transcripts revealed clear relationships to the associated tissue. For example, a search for retina-specific genes revealed that the ten most significantly associated with retina include five known genes, all related to retina function. Four are implicated in retina pathology: GNAT1 and ARR (night blindness), RHO (retinitis pigmentosa), and GUCA1A (cone dystrophy). Similar results were observed in numerous other tissues, although not as obviously related to pathology. The results appear especially striking for tissues with substantial EST representation, including brain, lung, liver, kidney, and testis, suggesting that putative tissue involvement can be inferred for many anonymous ESTs. Where possible, the tissue expression profile has been incorporated into the annotation of our gene index. Approximately half (50.5%) of the tissue-specific clusters were from embryonic tissue libraries (while such tissue contributed 6.2% of all UniGene ESTs). This striking result is consistent with the highly regulated and specific nature of embryonic development [40]. The embryo category is followed by brain (9.7% brain-specific versus 3.8% of ESTs) in number of tissue-specific clusters, kidney (5.5% versus 3.5%), and testis (6.1% versus 4.3%). We also examined the locations of the tissue-specific transcripts on the genome, and found no evidence of regional clustering (see description of regional functional clustering in Materials and methods).