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GermSAGE

http://germsage.nichd.nih.gov/

Description :
SAGE data on gene expression in male germ cell development

5 SAGE

http://5sage.gi.k.u-tokyo.ac.jp/

Description :
5 -end serial analysis of gene expression

SAGEmap

http://www.ncbi.nlm.nih.gov/SAGE

Description :
SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated by the Cancer Genome Anatomy Project (CGAP), which have been submitted to Gene Expression Omnibus (GEO). Gene expression profiles that compare the expression in different SAGE libraries are also available on the Entrez GEO Profiles pages. It is also possible to enter a query sequence in the SAGEmap resource to determine what SAGE tags are in the sequence, then map to associated SAGEtag records and view the expression of those tags in different CGAP SAGE libraries. SAGEmap provides a two-way mapping between SAGE tags and UniGene clusters. SAGEmap can also construct a user-configurable table of data comparing one group of SAGE libraries with another. SAGEmap is updated immediately following the update of UniGene. The data is also reflected in the human,mouse and rat genome Map Viewer as the SAGE track.

References :
Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF, SAGEmap: a public gene expression resource. Genome Research 2000 Jul;10(7):1051-1060. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10899154

PlasmoDB

http://plasmodb.org/

Description :
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species, and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE, and microarray projects. The relational schemas used to build PlasmoDB (GUS = Genomics Unified Schema and RAD = RNA Abundance Database) employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A version of the database is also available via CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.

Recent develoments :
Over the past year PlasmoDB has expanded to include new data and new data types as well as changes to the site. The highlights of recent developments are: Automated gene predictions for all genomic P. falciparum sequence. Gene expression data consisting of oligo- and cDNA-based microArray and SAGE experiments. Draft genomic, GSS, and/or EST sequence for four additional Plasmodium species: P. berghei, P. chabaudi, P. vivax, and P. yoelii. Cross-species comparison between P. falciparum and P. yoelii. Optical and microsatellite mapping data. Updated interface, news, and tutorial sections of web site.

Aknowledgement :
Financial support for PlasmoDB was provided by the Burroughs Wellcome Fund. Additional computational support was provided by Rahul Dave, Haralabos Tikos and the Eniac2000 project (supported in part through equipment donations from Intel). We thank the numerous researchers that have collaborated with and contributed to PlasmoDB by depositing data (both published and unpublished) in the database, by making software available, and by making useful suggestions on how to better improve this community resource. We wish to thank the scientists and funding agencies comprising the international Malaria Genome Project for making sequence data from the genome of P. falciparum (3D7) public prior to publication of the completed sequence. The Sanger Centre (UK) provided sequence for chromosomes 1, 3-9, & 13, with financial support from the Wellcome Trust. A consortium composed of The Institute for Genome Research, along with the Naval Medical Research Center (USA), sequenced chromosomes 2, 10, 11 & 14, with support from NIAID/NIH, the Burroughs Wellcome Fund, and the Department of Defense. The Stanford Genome Technology Center (USA) sequenced chromosome 12, with support from the Burroughs Wellcome Fund.

References :
1. Fletcher,C. (1998) The Plasmodium falciparum Genome Project. Parasitology Today, 14, 342-344.
2. The Plasmodium Genome Database Collaborative (2001) PlasmoDB: an integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Res., 29, 66-69.
3. Davidson, S., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G. C. and Stoeckert, C. J. Jr. (2001) K2/Klesli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal 40, 512-531.
4. Stoeckert, C., Pizarro, A., Manduchi, E., Gibson, M., Brunk, B., Crabtree, J., Schug, J., Shen-Orr, S. and Overton, C. G. (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17, 300-308.

Mouse SAGE

http://mouse.biomed.cas.cz/sage

Description :
SAGE libraries from various mouse tissues and cell lines

GOAL

http://microarrays.unife.it/

Description :
Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis.

SAGEmap

http://www.ncbi.nlm.nih.gov/SAGE/index.cgi

Description :
SAGE tag to gene mapping by NCBI.

SAGExplore

http://protein.bio.puc.cl/cardex/servers/sagexplore/home.php

Description :
SAGExplore is a tool for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE).

WebSage

http://bioserv.rpbs.jussieu.fr/websage/

Description :
WebSage is a tool that performs statistical analysis of SAGE data.

WebTraceMiner

http://www.conifergdb.org/software/wtm1.0/

Description :
WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3' and 5' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.

SAGE Home Page

http://www.sagenet.org/

Description :
Serial Analysis of Gene Expression; simultaneous expression and map information.

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