Data Sources:
	SAGE
	Microarray
Appendices:
	Data Tables

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SAGE

Serial Analysis of Gene Expression (SAGE) data is shown for normal corneal endothelium and Fuchs' endothelial dystrophy corneal endothelium. SAGE is a highly efficient method of gene expression analysis which relies upon the generation of unique, short (10 bp) sequences (tags) of cDNA which can be concatamerized, cloned, and sequenced. Tag sequences can serve as unique markers of larger genes due to the fact that a 10 bp sequence can distinguish between 1,048,576 transcripts given a random nucleotide distribution at the tag site.

Microarray

Microarray analysis of normal corneal endothelium was carried out in duplicate experiments. Microarrays are solid substrates to which known, nucleic acid sequences (probes) are placed in an ordered arrangement. Experimental samples of unknown nucleic acid sequences from cells or tissues of interest are labeled and exposed to the microarrays. If a probe on the microarray corresponds to a nucleic acid sequence in the experimental sample, complementary hybridization occurs and the probe sequence (corresponding to a specific gene) is thus identified as being present in the experimental sample. The microarray used in this experiment is the Affymetrix Hu95A array containing over 10,000 full-length human gene sequences. For more information on microarrays:

Data Tables

The CorneaNet system is built on a set of underlying database tables. Explanations of the sources and contents of each of those tables is included here.

Mapping Table 71909 records
This table was created by Elliott Margulies as part of his Ph.D. thesis at the University of Michigan and shows a single representative SAGE tag selected for each UniGene cluster based on an analysis of all ESTs within that cluster. The eSAGE package used to create this table is available online. Elliott is currently working at the National Human Genome Research Institute ( NHGRI) of the National Institutes of Health (NIH) in Bethesda, Md. Fields include: tag - SAGE 10-mer id description num sum count fit
Compare Table 8978 records
This table was created by Elliott Margulies and shows a comparison of SAGE experiment results for normal corneal endothelium compared to corneal endothelium from patients with Fuchs' Corneal Dystrophy. The table also contains some statistics comparing the results from the two conditions. Fields include: tag - SAGE 10-mer sage1 - expression in normal corneal endothelium sage2 - expression in Fuchs' corneal endothelium pval - significance of the difference in expression level for this SAGE tag between tissue 1 and tissue 2 sage1tosage2 -
Microarray 1 12558 records
This table shows data for an Affymetrix Hu95A microarray containing over 10,000 full-length human gene sequences, hybridised with a cDNA library constructed from normal, human corneal endothelium. Fields include: expressed - 'A' = absent, 'M' = maybe, 'P' = present for expression of the specified gene queried by the Affymetrix Hu95A microarray UniGene accession # - UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. description - drawn from NCBI databases
Microarray 2 12558 records
This table shows data for an Affymetrix Hu95A microarray chip containing over 10,000 full-length human gene sequences, hybridised with the same cDNA library analyzed by Microarray 1. Microarrays 1 and 2 are duplicate analyses of the same normal, human corneal endothelial cDNA library. Fields include: expressed - see above id - see above description - see above