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This form enables uploading of a file of SAGE tags, which are then matched against tags previously extracted from known datasets. 10 base pair (bp) tags for SAGE (17 base pair tags for longSAGE) were extracted from these files, based on the criteria of 3' most CATG, and/or polyA tail and/or poly A signals. (A polyA signal indicates a mature 3' untranslated region, formed by polyadenylation of the pre-mRNA). This aids with assigning tags to positions in the genome. All datasets with an asterix are updated weekly. Other datasets will be added as the site develops. If there is a particular dataset that you would be interested in seeing added to the site, please . To save your results, simply save the page and open in Microsoft Excel.

The file should be in the following tab-delimitedformat:
[yourlibraryidentifier_tagcount] [10 bp tag SAGE or 17 bp tag longSAGE]

For example:
mycortexlibrary_13 TTGGCGCTAG
mycortexlibrary_25 GTAAGCTGTA
mycortexlibrary_40 CCCTGAACAA

An example file can be found here.

Please upload a file of sage tags:
Please select a dataset to match your SAGE tags against:-
*NCBI Reference Sequence Collection: SAGE	reference sequence reviewed
	reference sequence provisional
	reference sequence predicted
	reference sequence model
	reference sequence known
*NCBI Reference Sequence Collection: longSAGE	LongSAGE : reviewed
	LongSAGE : provisional
	LongSAGE : predicted
	LongSAGE : model
	LongSAGE : known
LongSAGE tags mapped to genomic sequence
Pathways:	reelin pathway
	NFKB mediated signaling pathway
Gene families:	cell adhesion genes
	Microarray stem cell genes (SAGE)
	Ensembl genes (SAGE)
	Ensembl genes (longSAGE)
	ALzheimer genes
	[info] Neocortex genes
	[info] Cerebellum genes
	[info] RIKEN full length cDNAs
[info] SAGEmap reliable mappings	Short SAGE tags
	Long SAGE tags
All exon sequence aligned to genome	mRNA (source : UCSC)
Other complete databases	All MGI sequence

Details on the datasets used.

NCBI Reference Sequence Collection : SAGE

The NCBI Reference Sequence Collection is divided into five groups, partially to aid with determining higher quality matches, and partially to aid with speed. These are large databases and it would not be feasible to implement them as one database.

Reference Sequence : reviewed. The RefSeq record has been reviewed by NCBI staff. The review process includes reviewing available sequence data and frequently also includes a review of the literature. The genomic/mRNA/protein RefSeq records may have expanded sequence and annotation including addition of pubications and features, as deemed relevant. This dataset is the smallest of all of the RefSeq datasets.
[111 tags as of 23/05/2003]

Reference sequence : provisional. The RefSeq record has not yet been subject to individual review. The sequence-to-gene name associations have been established by outside collaborators and NCBI staff.
[10,846 tags as of 23/05/2003]

Reference Sequence : predicted. Some aspect of the RefSeq record is predicted and there is supporting evidence that the locus is valid. The existence of the mRNA is supported by existing cDNA, EST, and/or closely related homologous sequences. For mRNA/protein records, this status code primarily indicates that while a mRNA provides experimental evidence for the locus, the protein has been predicted.
[5,033 tags as of 23/05/2003]

Reference Sequence : model. This identifies the contig (NT_ accessions), mRNA (XM_), non-coding transcript (XR_) RefSeq records provided by the NCBI Genome Annotation process. These records are provided via automated processing.
[9,191 tags as of 23/05/2003]

Reference Sequence : known. Contains all reviewed, provisional and predicted records, including genomic regions (NG_) and those from the complete genomes project. Useful for quick identification of an entire SAGE library.
[15,972 tags as of 23/05/2003]

LongSAGE : reviewed. As for the SAGE reviewed, but composed of 17 bp (as opposed to 10 bp) tags

LongSAGE : provisional. As for the SAGE provisional, but composed of 17 bp (as opposed to 10 bp) tags

LongSAGE : predicted. As for the SAGE predicted, but composed of 17 bp (as opposed to 10 bp) tags

LongSAGE : reviewed. As for the SAGE reviewed, but composed of 17 bp (as opposed to 10 bp) tags

LongSAGE : model. As for the SAGE model, but composed of 17 bp (as opposed to 10 bp) tags

LongSAGE : known. As for the SAGE known, but composed of 17 bp (as opposed to 10 bp) tags

NFkB Database description.
Genes genes related to NFkB mediated signal transduction. Provides information on the expression profiles of the Rel/NFkB/IkB family, marker genes responsive to NFkB Signaling, related ligands/receptors and other genes involved in NFkB signal transduction

Gene Families

Cell adhesion genes. These SAGE tags were extracted from a collection which includes cell adhesion and extracellular matrix proteins, Integrins, Cadherin and Catenins, Selectins, Immunoglobulin (Ig) superfamily, Extracellular matrix proteins, Matrix metalloproteinases, Serine proteinases, Cystein proteinases, and Protease inhibitors.

Ensembl genes. These SAGE tags were extracted from the main gene set as predicted by Ensembl, which corresponds either to near full-length cDNA and/or protein sequences already available in the public sequence databases (known genes), plus novel evidence-based predictions (novel genes). The tags were taken from the mouse genome assembly version 3 [MGSC 11.3.1]. The id returned is the ensembl internal id.

Microarray stem cell genes. These SAGE tags were extracted from GEArray S Series Mouse Stem Cell Array from SuperArray. This array is designed to profile the expression of genes known to be important for the identification, growth and differentiation of mouse stem cells. The array contains over 260 known genes that encode markers of stem cells and their various stages of differentiation, growth factors and cytokines, extracellular matrix markers and other proteins. A total of 233 tags were extracted from this gene list.