TGP (based on the SRS system) allows for various types of queries, for example:
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Finding promoters that work in a particular plant species (entry field Target species, example 1);
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Finding promoters influenced by a particular regulator (entry field Regulator, example 2);
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Finding promoters that work in a particular plant species and are influenced by a particular regulator (fields Target species and Keywords and/or Regulator, example 3);
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Finding promoters isolated from a particular plant species (field PromoterID, example 4);
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Finding promoters influenced by several different regulators (example 5);
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Finding promoters that are active in a certain organ or tissue (fields STAGE_ORGAN_TISSUE and/or COMMENT); and
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Finding the tissue-specific promoters responsive to a particular regulator (searching the fields REGULATOR and STAGE_ORGAN_TISSUE or COMMENT).
Example 1
To find the promoters working in a particular plant species, click the field Target_species on the
home page of the TGP_PROMOTER table (marked by arrow 1 in Fig. 1) and then click the
button 
to see the list of transgenic species (currently, 27).
For instance, to find the promoters whose activities have been verified in barley, click barley (hordeum vulgare). This will result in a list of links (ID contains info on the corresponding species, e.g., Hv means Hordeum vulgare, Ta, Triticum aestivum or Td, Triticum turgidum subspecies durum). Check the list of promoters the expression of which has been evaluated in the specified organism.
Example 2
To browse the full list of regulators, the user has to click the field Regulator on the home page
of the TGP_PROMOTER table (Fig. 1, see above). On the next page, clicking on the button
will give a current list of regulators of the TGP database.
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For instance, to find the promoters influenced by low temperature, click cold to get the list of corresponding entries.
Example 3
To find the promoters that are active in a particular plant species and are influenced by
a particular regulator, the user has to click the button 
on the home page of the
TGP_PROMOTER table. This will result in a Standard query form for the TGP_PROMOTER
table (Fig. 2).
Figure 2. Standard query form for the TGP_PROMOTER table.
From the drop-down menu combine searches with, select AND (marked by arrow 1 in Fig. 2).
Select the field Target_species from the drop-down menu (arrow 2). In the text box, type the
species name (e.g., tobacco, arrow 3). Next, select the field Regulator from the drop-down
menu (arrow 2) and type the corresponding term in the text box (e.g., cold, arrow 3). Click the
button 
(arrow 4). This will give the list of promoters active in tobacco and influenced by cold.
Example 4
To find the promoters isolated from the particular plant species, select the data field PromoterID in the drop-down list box.
Input the first letters from the Latin name of the corresponding species (for example, Os means Oryza sativa, etc.), click the button and check the list of promoters.
Example 5
To find the promoters responsive to a few regulators, for example, ethylene and elicitor, select
AND from the drop-down menu combine searches with (Fig. 3). Select the field Regulator
from the drop-down menu (arrow 2). In the text-box to the right, type ethylene (arrow 3). Next,
select the field Regulator from the drop-down menu (arrow 2) and type the corresponding term
(e.g., elicitor, arrow 3). Click the button (arrow 4).
Figure 3. Standard query form for the TGP_PROMOTER table for a complex search.
This will result in two entries TGP_PROMOTER:Np:GN1_P1 and TGP_PROMOTER:At:PDF1.2_P1. Click on the entry to see the description of the promoter.
The user can also get the nucleotide sequence of the promoter of interest by clicking the SEQUENCE_ID link in the promoter entry. It is also possible to get the info on the corresponding gene (from which the promoter was isolated) by clicking the GENE_ID link.
Please note that Number of entries to display per page, can vary from 5 to 1000 by SRS standards.
Each promoter is supplied with description of the corresponding gene (from which it was isolated). Using a Standard query form for the TGP_GENE table, it is possible to
- Find the genes activated or repressed by a particular regulator (searching the fields KEYWORDS and ACTIVITY);
- Find the genes expressed in certain tissues or at certain stages of development (searching the fields KEYWORDS and ACTIVITY);
- Find the genes coding a particular protein (searching the field PRODUCT);
- Find the genes of a particular species from the currently available list (searching the field SPECIES); and
- Find the genes of a particular species activated by a particular inducer (searching the fields SPECIES, KEYWORDS, and ACTIVITY).
To find genes with the help of keywords, it is recommended to look at the full list of keywords. To do this, select Keywords in the list of TGP fields, input * and click the button List Values.
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and occur in at leastentries |
This will give the list of (currently) 103 keywords.
Select the keyword of interest (e.g., abscisic acid-repressed) and get an IDs list with the corresponding entries: TGP_GENE:At:CEL5 TGP_GENE:Hv:LEM2. To get more details, click hyperlinks.
Search for the genes by name
To find the gene by its name select the appropriate item in the drop-down list box. In the drop-down list select Gene and input the part of gene name with an asterisks (to make an extended search). For example, Delta1-pyrroline-5-carboxylate synthetase 1 gene was marked as p5csa, p5cs1, p5c*, etc.
you’ll get
the entry TGP_GENE:At:P5CSA.
Combinatory search
For example, to find a certain gene of a certain organism,the user can use two (or more) searching fields. In particular, to find the ferritin gene of A. thaliana, type mouse in the “Species” field and *fer* in the “Gene” field. It is possible to define the search details with the aid of logic operators: select the operator in the box: combine searches with .
Clicking You will get the TGP_GENE:At:Fer1 gene.
If you’ll define the BUTNOT operator (combine searches with ) ferritin genes of other organisms will be found: TGP_GENE:Gm:Fer, TGP_GENE:Zm:Fer1.
Searching for gene with a certain expression pattern
Search of the fields KEYWORDS and ACTIVITY can be used to find the genes expressed in certain tissues or at certain stages of development.