This webpage aims to provide all tools (or links to appropriate tools) to analyse SAGE and LongSAGE data beginning from the raw chromatograms. Read through the steps and begin at the one that is most appropriate to your stage of analysis. If you need additional explanations, leave a request via contact form at prime-essay.net.

Files of tags and their respective abundances (the tag count) can be analysed to determine which tags (and therefore which genes), are significantly expressed, by clicking here. The submitted file must be in the following format:

TAG             COUNT
TAGTGATGAG      12
CGTAGCACGT      3
GGTACCAGTA      34

TAG             COUNT_IN_LIBRARY_ONE    COUNT_LIBRARY_TWO       COUNT_IN_LIBRARY_THREE, etc
TAGTGATGAG      12                              36                      0
CGTAGCACGT      3                               17                      88
GGTACCAGTA      34                              2                       23

Once a SAGE tag has been assigned to a RefSeq gene, further information can be retrieved on the gene it was assigned to. To do this, simply upload your list of RefSeq accession numbers into this form. Further information on the genes of interest can be obtained from these websites:

Site		Description
Arrowsmith		Assists in looking for items or concepts that may be present in common between two distinct sets of articles. For example, it can aid in picking up distant relationships that a NCBI PubMed search may miss.
Biocarta		Pathways depicting molecular relationships, either browse by category or search by title.
FatiGO		FatiGO carries out simple datamining using GO. Input is either a list of Gene Symbols, or UniGene cluster ids.
GoFish		This is a java application that allows users to search for gene prodcuts with particular gene ontology attributes, or combinations of attributes. GoFish ranks gene products by the degree to which they satisfy a Boolean query.
GOstat		A web-based tool to annotate a large number of genes simultaneously using the vocabulary of gene ontology. Further information on the GO accession numbers (e.g. GO:0007186) can be found by searching the GO Browser at Mouse Genome Informatics.
iHOP		A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. This information system provides this network as a natural way of accessing the more than ten million abstracts in PubMed. Currently only set up to search one gene at a time.
PubGene Note - with the introduction of proprietary software, the free web public service is 12 months out of date	Gene Network Browser	Enables user selection of a gene, with the result that the literature neighbourhood around the gene is then shown. All information is extracted from the published literature.
SAGElist		A web interface to the mouse SAGE data published by Trendelenburg et al. (2002) Serial analysis of Gene Expression Identifies Metallothionein-II as Major Neuroprotective Gene in Mouse Focal Cerebral Ischemia. Journal of Neuroscience 22 (14):5879-5888. The data can be searched in several ways, including by using a tag or gene name.
Signal Transduction Knowledge Environment. Free registration is required to see these signal transduction connection maps. For further information, see the Science article .		•TNF Pathway •Fas Signaling Pathway •G alpha i Pathway [Gai] •G alpha s Pathway [Gas] •Gaq Pathway [Gaq] •Ga12 Pathway [Ga12] •Ga13 Pathway •T Cell Signal Transduction •B Cell Antigen Receptor •Estrogen Receptor Pathway •Wnt/ß-Catenin Pathway •TGF-ß Pathway •Differentiation Pathway in PC12 Cells •Jasmonate Biochemical Pathway •Cytokinin Signaling Pathway •Integrin Signaling Pathway •JAK-STAT Pathway •Interferon Pathway •STAT3 Pathway •Type 1 Interferon (IFNa/ß) Pathway •Phosphoinositide 3-Kinase Pathway
TAGmapper		Tagmapper is a comprehensive tool used to perform tag-to-gene mapping. It is built on the premise that a 10bp SAGE tag when derived from a definied position within the transcript, contains information sufficient enough to identify the corresponding gene. It promises to be an innovative and an user friendly tool that is built using open source software.
The WebQTL Project		A web site and database that can be used to systematically map gene loci (ATLs, modifiers) that modulate variation in the expression levels of transcripts. Entering a key word will give the expression data for that transcript, giving an indication of the expression with regard to genotype.

An alternative method of assigning information to tags is to use the Comparative Count Display software written at the NCBI, which can be used over the web here. This compares two libraries of tags and their abundances by generating a probability that the frequency of any tag in the distribution differs by more than a given fold factor from the other distribution.

There are various other tools available for use on SAGE data. A list of the more commonly available tools is shown below. If you are aware of any software missing from this list, please .

Tool	Brief summary
CSAGE	An open source UNIX/Linux tool written in C intended for the automated analysis of data generated with SAGE. Software and source are freely available. Please direct inquiries to .
eSAGE	A comprehensive software package for managing and analyzing data generated by SAGE, freely available for non-commerical use.
GeneX	An Open Source gene expression database and integrated tool set. Also see http://genex.ncgr.org/
POWER_SAGE	Program that can run 'virtual' SAGE studies with different combinations of sample size and tag frequency and determine the power for each combination - useful for planning SAGE experiments.
SAGE2000	SAGE2000 is freely available to academic investigators for non-commercial use.
SAGE Library Analysis	A method for predicting the reliability of low abundant SAGE tags that has been developed at Serono. The tool is in the form of a web page which allows you to upload a SAGE library and have it processed, for references see Colinge & Feger, Detecting the impact of sequencing errors on SAGE data, 2001, Bioinformatics, 17:840-842. The implementation is now available online at the following address: http://195.70.0.115/bioinf/sage/.
SAGElyzer	SAGElyzer is a R package for integrating gene expression data from various SAGE libraries, clustering transcripts on the basis of SAGE expression pattern, and annotating SAGE tags using pubic databases. For further information, please see the bioconductor listing or the pdf.
SAGEmap	NCBI's SAGEmap resource is a public resource for serial analysis of gene expression data. It is possible to retrieve information by use of: •a UniGene cluster id •a sequence with a GI number •a tag.
SAGEscreen	SAGEscreen is a multi-step procedure that addresses ditag processing, estimation of empirical error rates from highly abundant tags, grouping of similar-sequence tags and statistical testing of observed counts. SAGEscreen is available for academic users from slava.akmaev_at_genzyme.com. Reference: Correction of sequence-based artifacts in serial analysis of gene expression Akmaev and Wang, Bioinformatics 2004 20: 1254-1263 .
SAGEstat	A Windows executable compatible with all versions of Windows. To request a copy of this program please send an e-mail to [email protected] with the comment SAGEstat in the subject field. A description of the use of the program in planning SAGE experiments can be found in: Ruijter et al. (2002) Statistical evaluation of SAGE libraries: consequences for experimental design Physiological Genomics 11: 37-44. A second reference can be found in: Kal et al. (1999) Dynamics of Gene Expression Revealed by Comparison of Serial Analysis of Gene Expression Transcript Profiles from Yeast Grown on Two Different Carbon Sources. Molecular Biology of the Cell 10, 1859-1872.
TAGSEARCH	A computer program that can search for SAGE tags in genomic sequences.
USAGE	A web-based application for analysis of SAGE data. [Registration required].