About Our Database

Release date	August 14, 2006	Total number of genes	57,283
Total number of libraries	14	Protein coding	44,046
Annotation built on	BGI v1 vs. TIGR v4	Transposon related	13,237

Access to this web site and the gene expression data contained herein are provided for research purposes only. No commercial rights of any nature are granted. Parties interested in commercial applications should communicate with the Office of the Vice Provost for Research, University of Delaware, (302) 831-4230.

How To Use This Database

Queries can be made in several different ways. On this front page, the code for a specific gene may be entered below. Alternately, it is possible to explore the signatures in a particular region by entering a BAC name (the box below the gene code), or by clicking on the chromosome map at the bottom. It is also possible to enter a DNA sequence, extract all possible MPSS signatures from the sequence and then study the frequencies of those signatures in the libraries; for this option, please go to the page entitled "Query by Sequence."

What Is MPSS?

MPSS stands for Massively Parallel Signature Sequencing, a technique invented and commercialized by Solexa, Inc. of Hayward, California. MPSS and related technologies have been described in publications by Brenner et al. (Nature Biotechnol. [2000] 18:630-634, and PNAS [2000] 97:1665-1670). Like SAGE (Serial Analysis of Gene Expression), MPSS identifies short sequence signatures produced from a defined position within an mRNA, and the relative abundance of these signatures in a given library represents a quantitative estimate of expression of that gene. The MPSS signatures are 17 bp in length, and can uniquely identify >95% of all genes in rice.

Basic Queries

First choose a database for the mRNA data:

Next in the box below, enter specific information to retrieve MPSS map or data:

	Protein entry code (e.g. Os12g38210) Note:The TIGR "LOC_" prefix is not used in our database. Using an old ID? TIGR Version Converter	LOC_
	Contig name (e.g. Contig000021)
	Sequence of mRNA MPSS signature (e.g. GATCATATCTCCCATTC)
	Keyword for predicted protein function (e.g. actin)

Query by Chromosome Position

First choose a database:

Next click on a region of any chromosome for which you would like to retrieve the MPSS map. Because of the size of chromosomes, clicking on the diagram below will take you to a second map where you can refine the position.

Image of chromosomes