Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 69

Table 2.5 Integrative databases for Gene Expression analysis and technology in plants

Database Name Plant Species/Purpose Uniform Resource Locator

(URL)

Roche NimbleGen | Array
Synthesis

Roche platform; information on
MAS digital technology

http://www.nimblegen.
com/company/technol-
ogy/index.html

Roche NimbleGen Information website for biochip

technology

http://www.biochipnet.
com/node/146

Gene Expression Omnibus
(GEO) Main page

GEO navigation and browser
software—NCBI

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

AtGenExpress—Weigel
World

Microarray data and web informa-
tion for plant species

http://www.weigel-
world.org/resources/
microarray/
AtGenExpress/

TAIR—Gene Expression Micrarray data and gene expression,

and stress factors in Arabidopsis

http://arabidopsis.org/
portals/expression/
microarray/ATGenEx-
press.jsp

AtGenExpress JPN (Arabi-
dopsis Gene Expression
profile data base) | Data-
base Registry | RIKEN

Arabidopsis gene expression profile
data base from RIKEN

https://database.riken.
jp/sw/en/AtGenEx-
press_JPN_(Arabidop-
sis_Gene_Expression_
profile_data_base)/
crib151s2rib151s85i/

ATTED-II: Home Site for the co-regulation gene func-

tions; mainly in Arabidopsis and
rice

http://atted.jp/

GENEVESTIGATOR—The
gene expression search
engine

Site for the search engine—Gene-
investigator; biomedical, plant
biology

https://www.genevestiga-
tor.com/gv/

The BAR and other Data
Analysis Tools for Plant
Biology

Bio Array resource for plant biology;
number of crop plants

http://bar.utoronto.ca/
welcome.htm

http://www.bar.utoronto.
ca/3DDI/

3D data display initiative for large
scale dataset display

http://3ddi.org/

http://www.arexdb.org/ Arabidopsis gene expression data

base web site

http://www.arexdb.org/

Yale Rice Project Whole genome transcription profile

for rice cells, tissues

http://bioinformatics.med.
yale.edu/riceatlas/

Tiling Array, Tiling primers
& probes, design prim-
ers for tiling, amplify
whole genome tiling
arrays

Design whole genome primers for
use in array design, including
DNA methylation

http://www.premierbiosoft.
com/dnamicroarray/til-
ing_array.html

Tiling Arrays, Library File
Updates | Affymetrix

GeneChip tilling array, software and
analysis

http://www.affymetrix.
com/support/technical/
libraryfileupdatesmain.
affx

Arabidopsis thaliana—Til-
ing Array Express—
Weigel World

Arabidopsis tilling array express;
genome browser and used for
visual cross platform comparison

http://www.weigel-
world.org/resources/
microarray/at-tax