Experimental annotation of the human genome using microarray technology

Shoemaker, Daniel; Schadt, Eric E.; Armour, Christopher D.; He, Yudong; Garrett-Engele, Philip W.; McDonagh, Paul; Loerch, Patrick; Leonardson, Amy; Lum, Pek Yee; Cavet, Guy; Wu, Lani F.; Altschuler, Steven J.; Edwards, Stephen A.; King, Justin W.; Tsang, J. S.; Schimmack, Greg; Schelter, Janell M.; Koch, John E.; Ziman, Michael; Marton, Matthew J.; Li, B.; Cundiff, Paige; Ward, Teresa R.; Castle, John C.; Krolewski, M. A.; Meyer, Michael; Mao, M.; Burchard, Julia; Kidd, M.; Dai, Hongyue; Phillips, John W.; Linsley, Peter S.; Stoughton, Roland; Scherer, Stewart; Boguski, Mark S.

doi:10.1038/35057141

Cited by 404 publications

(255 citation statements)

References 28 publications

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“…In 2001, the false positive rate for Genscan was estimated on chromosome 22 using microarray analysis. This study concluded a false positive fraction of 17% compared to the original estimate by the chromosome 22 sequencing group of 27.5% [12,13]. Using this assumption and predicting that the rate is constant over the other chromosomes, this would mean that 7368 (0.17 · 43 000) genes from the whole Genscan set of 43 000 genes are false predictions.…”

Section: Introductionmentioning

confidence: 97%

Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery

et al. 2004

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Large amounts of refined sequence material in the form of predicted, curated and annotated genes and expressed sequences tags (ESTs) have recently been added to the NCBI databases. We matched the transcript-sequences of RefSeq, Ensembl and dbEST in an attempt to provide an updated overview of how many unique human genes can be found. The results indicate that there are about 25 000 unique genes in the union of RefSeq and Ensembl with 12-18% and 8-13% of the genes in each set unique to the other set, respectively. About 20% of all genes had splice variants. There are a considerable number of ESTs (2 200 000) that do not match the identified genes and we used an in-house pipeline to identify 22 novel genes from Genscan predictions that have considerable EST coverage. The study provides an insight into the current status of human gene catalogues and shows that considerable refinement of methods and datasets is needed to come to a conclusive gene count.

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Section: Introductionmentioning

confidence: 97%

Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery

et al. 2004

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“…Recent advances in genome sequencing programs coupled with advances in gene expression technology have provided tools to perform comprehensive, quantitative comparisons at the transcriptional level of thousands of genes simultaneously. Currently, gene microarrays can be constructed with cloned cDNA probes (24) or with synthetic oligonucleotide probes (25,26). By labeling cellular RNA and monitoring hybridization to arrayed probes, this technology provides the opportunity to thoroughly evaluate the processes of hepatocyte dedifferentiation and adaptation.…”

Section: Introductionmentioning

confidence: 99%

Temporal Gene Expression Analysis of Monolayer Cultured Rat Hepatocytes

Baker

Carfagna

Gao

et al. 2001

Chem. Res. Toxicol.

134

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The use of cultured primary hepatocytes within toxicology has proven to be a valuable tool for researchers, however, questions remain with regard to functional differences observed in these hepatocytes relative to the intact liver. Cultured hepatocytes have typically been described as dedifferentiated, a classification based upon the investigation of a few key cellular processes or hepatocellular markers. In the present study, parallel expression monitoring of approximately 8700 rat genes was used to characterize mRNA changes over time in hepatocyte cultures using Affymetrix microarrays. We isolated and labeled mRNA from whole rat livers, hepatocyteenriched cell pellets, and primary cultured hepatocytes (4,12,24,48, and 72 h postplating), and hybridized these samples to microarrays. From these data, several pairwise and temporal gene expression comparisons were made. Gene expression changes were confirmed by RT/ PCR and by performing replicate experiments and repeated hybridizations using a rat toxicology sub-array that contained a 900-gene subset of the 8700-gene rat genomic microarray. PCR data qualitatively reproduced the temporal patterns of gene expression observed with microarrays. Cluster analysis of time course data using self-organizing maps (SOM) revealed a classic hepatocyte dedifferentiation response. Functional grouping of genes with similar transcriptional patterns showed time-dependent regulation of phase I and phase II metabolizing enzymes. In general, cytochrome P450 mRNA expression was repressed, but expression of phase II metabolizing enzymes varied by class (upregulation of glucuronidation, downregulation of sulfation). Potential metabolic targets for toxic insult, such as glutathione metabolism, gluconeogenesis, and glycolysis, were also affected at the transcriptional level. Progressive induction of several genes associated with the cellular cytoskeleton and extracellular matrix was observed in accord with physical changes in cell shape and connectivity associated with cellular adhesion. Finally, many transcriptional changes of genes involved in critical checkpoints throughout the hepatocyte cell cycle and differentiation process were observed. In total, these data establish a more comprehensive understanding of hepatocellular dedifferentiation and reveal many novel aspects of physiological and morphological hepatocyte adaptation. An assembly of all transcripts that demonstrated differential expression in this study can be found in the Supporting Information.

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“…" 3 . Annotation aided by geneexpression microarrays was fast gaining attention, Schadt says, "and we just thought we were going to make it big".…”

Section: Friends Reunitedmentioning

confidence: 99%