RnR Regulatory-network Research in Arabidopsis T87 cultured cells

Published at 20081201, renewed at 20091224

The 185 over-expression experiments in Arabidopsis T87 cultured cells are presented.

Click here to access to the old RnR database.

RnR is ...

a database for over-expression experiments in Arabidopsis T87 cultured cells. In our project, we obtained and constructed approx. 2000 RAFL clones (by RIKEN) of the genes on which we focused. We selected approx. 185 constructs that we expected to relate to metabolism and utilized for analyses using DNA microarray (214 assays, 214 experiments), GC-MS (1118 assays, 222 experiments), UPLC-MS (1006 assays, 201 experiments), and CE-MS (990 assays, 196 experiments). The RnR database provides the results of such analyses for understanding the large-scale regulation relationships of gene expression and metabolite accumulation in plants.

Requirements

  • _Checked Browser: Internet Explorer (8.0; 7.0; 6.0 SP2, SP3), Firefox (3.6; 3.5), Opera (10.10), Safari (4.0), Google Chrome (4.0)
  • _Checked OS: Microsoft Windows XP (Pro. 2002 SP2, SP3; Home Premium SP2, Home 2002 SP2, Sp3), Vista Ultimate (SP2), Linux Fedora 12, Macintosh OS X (10.4, 10.5)

How to use RnR

  • _ RnR allows a user to retrieve gene-to-gene and gene-to-metabolite regulatory relationships when a user submits a gene or metabolite of interest.
  • _ RnR provides 4 ways to submit a query:
    1. input a query (see Examples), according to the below Retrieval form;
    2. click the below regulatory network image to select a node (dot) of interest;
    3. click the below pie charts of over-expressed genes and metabolites to select a gene or metabolite of interest;
    4. click the links just above the pie charts to select a gene or metabolite in tables of over-expressed genes.
  • _ In any regulatory networks and modules, nodes representing genes or metabolites are clickable to jump to the page of a gene or metabolite of interest.

Regulatory network T87 cell stereograph
Over-expressed genes Over-expressed genes

Retrieval form

1. Input query word (e.g. At5g61420, stress, C2H5NO2, 75.0320)

_Examples

2. Submit (Click the below image)

Links

KAGIANA KAGIANA: an Excel-based tool for retrieving functional description of Arabidopsis genes
MassBase MassBase: a database for characterizing plant metabolites
CoP CoP: a database for analyzing co-expression of plant genes

Department of Biotechnology Research
Kazusa DNA Research Institute

Maintained by
Yoshiyuki Ogata (yogata@kazusa.or.jp)

Copyright (C) 2007-2010 All rights reserved Kazusa DNA Research Institute