Tools
TRABAS contains
three tools/search pages for data retrieval and analysis
Search by
expression tool
User gene list search tool
Users
can also retrieve expression and other information, for a set of
genes of their interest, from TRABAS by using the tool. The
required input for this tool is a set of AGI codes.
Array search tool
The
ABA signaling related microarrays integrated in TRABAS were based on
different microarray platforms(8k microarrys, 25k microarrays and cDNA
microarrays) therefore genes which are present and induced/repressed in
one array may be absent in other arrays. Moreover for data derived from
different publications information for only those genes which show
expression change above a threshold(selected by respective authors)
are available. Therefore the "-" can be indicative of
non-induction/repression as well as absence of gene in the particular
array. To discriminate these two possibilities we have included the
array search tool into TRABAS. This tool takes as input a set of
genes(in form of a list of AGI codes) and reports the presence and
absence of these genes in different types of arrays.
Array Details
The
experiments
included in TRABAS were derived from various sources and contain
arrays of different types. A summary of different slides and arrays and
genes contained in them are given below.
Source
|
Author/Database |
Array/Experiment
type |
Data type
|
Number of
genes
|
| PUBLICATION |
Xin(2005) |
ATH1 |
Log 2 of
Fold Change |
22500 |
| PUBLICATION |
Li(2005) |
ATH1 |
Fold change |
22500 |
| PUBLICATION |
Seki(2002) |
cDNA |
Fold change |
~7000 |
| PUBLICATION |
Hoth(2002) |
MPSS |
Fold change |
expected to
include all genes
|
| TAIR/ATTED |
ME00333 |
ATH1(25K) |
Log 2 of
Fold Change |
22500 |
| TAIR/ATTED |
ME00351 |
ATH1(25K) |
Log 2 of
Fold Change |
22500 |
| PUBLICATION |
Suzuki(2003)
|
Affymetrix-8k
|
Fold change |
~7000 |
| PUBLICATION |
Sanchez(2005)
|
ATH1(25K) |
Fold change |
22500 |
| PUBLICATION/TAIR
|
Leonhardt(2004)
|
Affymetrix-8k
|
Fold change |
~7000 |
Normalized
and
log transformed expression data for experiments in the abiotic and
biotic stresses, chemical and hormone treatment and development
categories were downloaded from the ATTED database. All of these studies
were performed on affymetrix 25k (ATHI) arrays containing ~22000
genes. The summary of normalization and other processing methods can be
found in the help section of the ATTED database.
Reference and Links
Microarray
Experiments
Hoth
S, Morgante M ,Sanchez JP, Hanafey MK, Tingey SV,Chua NH (2002)
Genome wide expression profiling in Arabidopsis thaliana reveals new
targets of abscisic acid and largely impaired gene regulation in the
abi1-1 mutant. J.Cell Sci 115:4891-4900
Leonhardt N, Kwak JM
,Robert N, Warner D, Leonhardt G, Schroeder JI(2004) Microarray
expression analyses of Arabidopsis guard cells and isolation of a
recessive abscisic acid hypersensitive protein phosphatase 2C mutant.
Plant Cell 16: 596-615
Li Y, Lee KK, Walsh S,
Smith C,
Hadingham S, Sorefan K, Cawley G, Bevan MW.(2006) Establishing
glucose- and ABA-regulated transcription networks in Arabidopsis by
microarray analysis and promoter classification using a Relevance
Vector Machine.Genome Res ;16(3):414-27.
Sanchez,
J. P.,Duque, P.,Chua, N. H. (2005) ABA activates ADPR cyclase and
cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant
J. ;381-95.
Seki M, Ishida J,
Narusaka M, Fujita M, Nanjo T,
Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama
K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y,
Shinozaki K.(2002) Monitoring the expression pattern of around 7,000
Arabidopsis genes under ABA treatments using a full-length cDNA
microarray. Funct Integr Genomics. ;2(6):282-91.
Suzuki M,
Ketterling MG, Li Q-B, McCarty DR (2003) VP1 alters global gene
expression patterns through regulation of ABA signaling. Plant
Physiol 132: 1664–1677
Xin
Z, Zhao Y, Zheng ZL (2005) Transcriptome analysis reveals
specific
modulations of abscisic acid signaling by ROP10 small GTPase in
arabidopsis. Plant Physiol 139:1350-1365
Obayashi
T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D,
Saito K, Ohta H. (2007) ATTED-II: a database of co-expressed genes and
cis elements for identifying co-regulated gene groups in Arabidopsis.
Nucleic Acids Res., D863-D869.
Gene Ontology
Ashburner,
M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M.,
Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A.,
Hill, D.P., Issel-Tarver. L., Kasarskis, A., Lewis, S., Matese, J.C.,
Richardson, J.E., Ringwald, M., Rubin, G.M. and Sherlock, G. (2000)
Gene ontology: tool for the unification of biology. The Gene Ontology
Consortium. Nat Genet. 25: 25-29.
Cis regulatory elements
PLACE database ( (www.dna.affrc.go.jp/PLACE/)
K. Higo, Y. Ugawa, M. Iwamoto and T. Korenaga (1999) Plant
cis-acting regulatory DNA elements (PLACE) database Nucleic Acids
Research Vol.27 No.1 pp. 297-300.
ATCISDB database
(http://arabidopsis.med.ohio-state.edu/AtcisDB/)
Molina, C., and Grotewold, E.(2005) Genome wide analysis of
Arabidopsis core promoters BMC Genomics., 6:25.
Ontology
and upstream sequence data :
Gene ontology annotations and
1Kb upstream sequence of all Arabidopsis genes were downloaded from TAIR
www.arabidopsis.org