TRABAS help


Information for ABA regulated genes can be retrieved on the basis of any of the following

Retrieve data by expression behavior

The first four parameters can be used for retrieving genes which show induction/repression above/below a fold cutoff in a particular microarray slide. Please remember when the corresponding filter is not required the filter should be in off (none) mode.

Parameter

Options

Effect

Score filter

ON

the expression score filter is active and the program selects out genes which show upregulation or downregulation (depending on the selected value from the "type" menu) greater than the user selected cutoff (depending on selected value from the "fold cutoff" menu) in the selected slide(depending on selected slide from the "slide" menu)

OFF
 the expression score filter is inactive

Slide*

Slide names

select a slide which will be used to filter genes

Type

U

retrieves upregulated genes (which show induction is above the selected cut-off folds)

D

retrieves down regulated genes (which show repression below the selected cut-off folds)

Fold Cutoff

1,2,3,4,5

Cutoff value in terms of fold change which will be used to retrieve up/down or regulated genes




*slides which can be used for filtering genes:
Slide Name Source
Hoth_ABA50_mM_3#5hours Hoth(2002)
Li_ABA_10uM_0#6hours Li(2006)
ME00333_ABA_10uM_1hours TAIR microarray experiment ME00333
ME00333_ABA_10uM_30minutes TAIR microarray experiment ME00334
ME00333_ABA_10uM_3hours TAIR microarray experiment ME00335
ME00351_ABA_30uM_24hour TAIR microarray experiment id ME00351
ME00351_ABA_3uM_24hours TAIR microarray experiment id ME00352
seki_ABA_100uM_01h Seki(2002)
seki_ABA_100uM_02hours Seki(2002)
seki_ABA_100uM_05h Seki(2002)
seki_ABA_100uM_10h Seki(2002)
seki_ABA_100uM_24h Seki(2002)
xin_ABA_1uM_4h Xin(2005)




Retrieve data by expression class

Studies on ABA signaling have identified various groups of ABA regulated genes on the basis of expression of genes in multiple slides(like mutant vs wild type, different time courses points). To facilitate the retrieval of such information (which is not possible by filtering genes by expression type and cutoff in a single slide) we have included the "Class Filter" option in TRABAS.

To retrieve expression data/other information for genes which belong to a particular ABA regulated sub group the "Class Filter" should be turned to "ON" and the corresponding class* should be selected from the "Class ID" menu . This filter can be used in combination with expression score filter or can be used exclusively.


*The list of classes (included in the class ID menu) along with a brief description of the class and the source from which the class was derived :-

Class
 Description Reference
Time_IL Time course expression group (late upregulation) Seki et al (2002)
Time_IRC Time course expression group (rapid and constant upregulation)
Time_IRT Time course expression group (rapid and transient upregulation)
Tissue_IMG Genes upregulated in both mesophyll and gaurd cell Leonhardt et al (2004)
Tissue_IMO Genes upregulated in mesophyll but not in gaurd cell
Tissue_IGO Genes upregulated in gaurd cell but not in mesophyll
Tissue_RGO Genes downregulated in gaurd cell but not in mesophyll
Tissue_RMO Genes downregulated in mesophyll but not in gaurd cell
Suzuki_Group_1 ABA_dependent_Activated_VP1_enhanced Suzuki et al (2003)
Suzuki_Group_2 ABA_dependent_Activated_VP1_suppressed
Suzuki_Group_3 ABA_dependent_repressed_VP1_enhanced
Suzuki_Group_4 ABA_dependent_repressed_VP1_suppressed
Suzuki_Group_5 ABA_regulated_Activated
Suzuki_Group_6 ABA_regulated_Repressed
Suzuki_Group_7 VP1_AND_ABA_dependent_Repressed
Suzuki_Group_8 VP1_AND_ABA_dependent_activated
Suzuki_Group_9 VP1_activated_ABA_activated
Suzuki_Group_10 VP1_activated_ABA_repressed
Suzuki_Group_11 VP1_dependent_Activated_ABA_enhanced
Suzuki_Group_12 VP1_dependent_Activated_ABA_suppressed
Suzuki_Group_13 VP1_dependent_Repressed_ABA_enhanced
Suzuki_Group_14 VP1_dependent_Repressed_ABA_suppressed
Suzuki_Group_15 VP1_regulated_Activated
Suzuki_Group_16 VP1_regulated_Repressed
Suzuki_Group_17 VP1_repressed_ABA_activated
Suzuki_Group_18 VP1_repressed_ABA_repressed
Xin1 Genes induced by ABA in wild-type (Ws) but not in rop10-1 Xin et al (2005)
Xin2 Genes induced by ABA in rop10-1but not in wild-type (Ws)
Xin3 Genes with higher expression in ABA-treated rop10-1 than in ABA-treated Ws
R1 Repressed in 1 experiments Classes derived from comparison of ABA mediated gene induction and repression in different experiments
R2 Repressed in 2 experiments
R3 Repressed in 3 experiments
I1 Induced in 1 experiments
I2 Induced in 2 experiments
I3 Induced in 3 experiments
I4 Induced in 4 experiments
I5 Induced in 5 experiments
IR Genes induced and repressed by ABA






Retrieve data by user provided gene list

User can also use TRABA to retrieve information related to the expression of their own set of genes in ABA signaling related experiments, and other microarrays as well as the distribution of known CREs and Gene Ontology terms in the gene set by providing the set of AGI of codes in the input box of "trabas user data search page "(www.bioinformatics.org/trabas/trabas_user_data) .
Sample Geneset


Data to Output

The parameter “Data to Ouput” can be used to select the type of information that is the retrieved for the set of genes which were selected with the help of the filters (score filter/class filter).

The options in "Data to Output" menu include the following:

a) Expression in ABA related microarrays

Category Description Expression slides
ABA wild type only
 13 slides from five experiments related to ABA signaling in wild type Arabidopsis

ABA all experiments
 22 slides from experiments related to ABA signaling in wild type Arabidopsis all_slides


b) Expression in other array categories
Category Description link
Abiotic Stress
 Abiotic stress related microarray slides from TAIR
abiotic_slides
Biotic stress
 Biotic stress related microarray slides from TAIR
 biotic_slides
Chemical treatment
 Chemical treatment related microarray slides from TAIR
 chemical_slides
Hormone treatment
Hormone treatment related microarray slides from TAIR
 hormone_slides
Development
 Development related microarray slides TAIR
 development_slides


c) Other Information


Option
 Description
 Data processing
GOBP Gene Ontology Biological Process
 Retrieves available GOBP annotation** of genes ( from the selected gene set) and compares the occurrence of each GO annotation term in the selected gene set to the GO terms occurrence in background ( all arabidopsis genes).
GOMF Gene Ontology Molecular Function Retrieves available GOMF annotation** of genes ( from the selected gene set) and compares the occurrence of each GO annotation term in the selected gene set to the GO terms occurrence in background ( all arabidopsis genes).
GOCC Gene Ontology Cellular Component Retrieves available GOCC annotation** of genes ( from the selected gene set) and compares the occurrence of each GO annotation term in the selected gene set to the GO terms occurrence in background ( all arabidopsis genes).
PLACE_motifs
 Known Cis regulatory elements from the PLACE database
 Scans 1Kb upstream sequence* of genes ( from the selected gene set) with each CRE from the PLACE database and compares the occurrence of each CRE in promoters of  the gene set to the CREs occurrence in background ( 1Kb upstream sequence of all arabidopsis genes).
ATCISDB_motifs Known Cis regulatory elements from the ATCISDB database Scans 1Kb upstream sequence* of genes ( from the selected gene set) with each CRE from the PLACE database and compares the occurrence of each CRE in promoters of  the gene set to the CREs occurrence in background ( 1Kb upstream sequence of all arabidopsis genes).

*1Kb upstream nucleotide sequences based on TAIR7 were downloaded from TAIR database
**GO classes which contain at least eight Arabidopsis genes are included in search

Setting this parameter to “hormone_treatment” for example will retrieve expression of the gene set in hormone treatment experiments. Selection of the option "GOBP annotation" from this menu will similarly direct the program to retrieve and summarize GOBP (gene ontology) annotations of the set of genes.

Sample Output of TRABAS gene search

elect Slide Hoth#ABA 50_nM_# 3#5hours* Hoth# abi1_mutant* Li# ABA# 10uM# 0#6hours* ME00333# ABA# 10uM# 1hours ME00333#ABA# 10uM# 30minutes ME00333# ABA#10uM #3hours ME00351# ABA# 30uM# 24hours ME00351# ABA# 3uM# 24hours Sanchez# ABA# 2h* Sanchez# ABA# 6h* Sanchez# cADPR# 6h* Seki# ABA# 100uM# 01h* Seki# ABA# 100uM# 02hours* Seki# ABA# 100uM# 05h* Seki# ABA# 100uM# 10h* Seki# ABA# 100uM# 24h* Suzuki# ABA_effect_ abi3* Suzuki# ABA_effect_ VP1* Suzuki# abi3_ noABA* Suzuki# abi3_ plusABA* Xin# ABA# 1uM#4h* Xin# rop10mutant*
At1g01720 - - 2.56 1.47 1.34 1.14 -0.03 -0.58 3.48 - - 4.7 5.0 3.6 4.8 6.0 - - - - - -
At1g69490 - - 19.53 0.33 -0.21 2.91 0.39 0.56 2.46 - - 5.8 9.8 8.0 8.8 10.2 4.61 1.42 1.30 0.39 - -
At1g71960 - - 3.56 0.77 -0.51 1.65 0.62 0.44 - - - 4.9 4.5 4.3 6.0 5.7 - - - - - -
At1g73480 5.35 2.88 5.56 1.86 -0.08 2.69 -0.08 -0.10 - - - 7.1 6.4 4.9 4.6 5.5 - - - - 3.3 5.0
At1g78070 - - 3.27 1.49 0.54 1.62 -0.56 -1.01 - - - 6.6 4.6 2.9 4.9 4.2 - - - - 3.1 2.7
At2g15970 17.69 3.49 - 0.58 -0.18 1.28 1.02 0.27 4.29 4.6 - 6.2 8.9 6.7 7.8 5.3 - - - - 2.7 2.5
At2g34560 - - - -0.06 -0.23 0.24 0.06 -0.16 - - - 4.3 3.8 3.1 5.5 3.6 - - - - - -
At3g11420 11.00 1.79 6.74 0.40 -0.62 2.43 -0.60 -0.80 2.46 - - 5.1 4.2 3.0 4.9 4.7 - - - - 2.6 2.7
At3g15670 23.0 5.00 56.95 -0.56 -0.97 4.47 0.12 -0.02 32 64.0 - 3.0 4.0 5.4 4.5 4.8 1.43 168.97 3.47 263.43 - -
At4g16760 4.67 -1.08 3.66 -0.12 -0.21 0.93 -0.20 -0.18 - - - 3.8 6.0 5.0 5.4 4.2 - - - - - -
At4g26080 16.37 3.02 4.05 1.57 0.69 2.12 0.26 0.20 7.46 4.6 3.03 - - - - - 3.64 1.00 0.76 0.24 3.5 4.1
At4g27410 87.67 3.54 6.99 1.89 0.54 2.87 -0.98 -1.29 8 4.9 - 14.2 15.0 12.9 18.6 22.3 4.51 1.18 1.04 0.25 4.6 5.0
At4g34230 4.77 8.50 2.95 0.12 -0.31 1.86 -0.03 0.23 3.73 2.1 - 6.7 5.8 4.9 7.8 5.8 - - - - - 2.4
At5g07440 - - - 0.14 0.07 -0.19 0.08 -0.02 2.46 - - 4.8 7.5 5.9 5.4 4.4 - - - - - -
At5g09440 - - - 0.43 -0.03 0.28 -0.18 0.36 3.03 - - 4.6 5.2 3.0 4.5 4.5 - - - - - -
At5g15960 24.0 6.00 5.17 0.94 -0.74 2.80 0.97 0.12 4.29 4.0 3.2 6.8 9.8 9.2 9.6 6.0 5.35 5.33 0.95 0.96 4.5 3.5
At5g15970 6.24 4.55 - - - - - - - - - 6.2 9.5 8.8 8.9 5.8 - - - - - -
At5g20230 - - - -0.54 0.06 1.13 -0.65 -0.52 3.25 4.0 5.66 7.4 7.0 5.3 5.8 4.7 - - - - - -
At5g59820 3.36 1.20 - 0.21 -0.01 0.74 0.16 -0.10 2.83 - - 6.9 5.7 4.0 7.0 6.4 - - - - - -
At5g63790 5.67 1.67 - 0.77 0.97 0.82 -0.30 -0.82 3.48 - - 4.3 4.7 3.0 5.3 3.6 - - - - - -
At5g64260 - - - 0.90 -0.01 1.25 0.05 -0.22 7.46 - - 4.2 5.4 4.4 5.5 4.0 - - - - - -


Induced greater than 2 fold
2.34
repressed greater than 2fold
-3.42

                                                                                
Slides names containing '*'
fold change
Other slides
Log base 2 of fold change


information for expression of the gene in the selected slide not available
(The gene is either not induced/repressed or absent in the array)
-


As the studies on ABA signaling included in TRABAS were performed on different microarrays (see next section), the set of genes included in each study was not same. Therefore for many genes while the expression in some arrays is known we do not have information about how the gene is expressed in other arrays. Such cases are indicated with a "-" sign. 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 the user can apply array search tool (www.bioinformatics.org/array_search) . The array search tool takes as input a set of genes and reports the presence and absence of these genes in different types of arrays.