TUTORIAL OF TGP DATABASE


Database organization
Format
How to use TGP

Database organization

TGP is implemented on the SRS (Sequence Retrieval System) platform and consists of three cross-linked constituent tables: TGP_GENE, TGP_PROMOTER and TGP_SEQUENCE. Detailed description of table fields is given in the section Format.

Format

TGP_GENE

Table of genes (TGP_GENE) contains general information on the activity and tissue-specificity of the genes whose promoters are offered for the transgene design. This table contains following fields:

GENE_ID This identifier is unique within TGP_GENE. Each gene described is marked with genus species abbreviation and gene abbreviation

DATE Data of the last editing, consisting of day, month, year

AUTHOR Annotator’s name

GENE Short, full and synonym names of the gene

PRODUCT Full, short and synonym names of the gene product

TAXON Taxonomy classification of the species

SPECIES Common and Latin names of the organism

KEYWORD Key words

ACTIVITY Common description of the gene functional activity

PROMOTER_ID Cross-references to the PROMOTER_ID in the TGP_PROMOTER table

SEQUENCE_ID Cross-references to the SEQUENCE_ID in the TGP_SEQUENCE table

REFERENCE Bibliographic reference

PUBMED EntrezPUBMED cross-reference

END The end of the entry to the TGP_GENE

EXAMPLE:

GENE_ID Pc:PR2                                                                                                 

DATE 15.02.2006

AUTHOR Smirnova O.

GENE pr2

PRODUCT pathogenesis-related protein 2

TAXON Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Apiales; Apiaceae; Apioideae; apioid superclade; Apium clade; Petroselinum.

SPECIES parsley, Petroselinum crispum

KEYWORD pathogenesis, elicitor inducible

ACTIVITY A 20- to 50-fold increase in the level of PR2 mRNA occurs within the first 3 h following addition of fungal elicitor to the cells.

PROMOTER_ID Pc:PR2_P1 Pc:PR2_P2

SEQUENCE_ID Pc:PR2_P1S Pc:PR2_P2S

REFERENCE van de Locht U., Meier I., Hahlbrock K., Somssich I.E. A 125 bp promoter fragment is sufficient for strong elicitor-mediated gene activation in parsley. EMBO J., 1990, 9, 2945-2950.

PUBMED 2390976

END

TGP_PROMOTER

This table accumulates information on functionally active promoters described in annotated scientific sources and contains following fields:

PROMOTER_ID This identifier is unique within TGP_ PROMOTER. Each PROMOTER described is marked with genus species abbreviation, gene abbreviation and promoter number

GENE_ID Cross-reference to corresponding GENE_ID in the TGP_GENE table

GENE Short, full and synonym names of the gene

LOCALIZATION The field describes promoter localization according to the start of transcription (ST) or translation (SR) and promoter localization according to the EMBL sequence numeration

DESCRIPTION Description of the promoter construction has been used

SEQUENCE_ID Cross-reference to the SEQUENCE_ID in the TGP_SEQUENCE table

REPORTER Name of the product used to estimate the expression level of the promoter (reporter enzymatic activity, protein or mRNA)

SPECIFICITY Name of the transgenic organism, its developmental stage and organs used for the promoter expression

INDUCER Inductor or repressor names, its concentrations and duration of the signal effect used in experiment

COMMENT Comment on the expression pattern of the promoter; organs, tissues and cells of transgenic organism where the promoter expression is described

REFERENCE Bibliographic reference

PUBMED EntrezPUBMED cross-reference

END The end of the entry to the TGP_PROMOTER

EXAMPLE:

PROMOTER_ID Pc:PR2_P1

GENE_ID Pc:PR2

GENE pr2

LOCALIZATION from -168 to +229; EMBL; X55736; ST: 791; from 623 to 1019

DESCRIPTION The region upstream of CDS of the reporter gene included the promoter region of the pr2 gene (168 bp upstream of transcription start site), 103 bp of 5'UTR and 126 bp of CDS of the psl gene.

SEQUENCE_ID Pc:PR2_P1S

REPORTER GUS activity

SPECIFICITY transgenic parsley protoplasts

INDUCER elicitor (8 h)

COMMENT An 8-fold increase in GUS activity was measured in elicitor-treated versus untreated protoplasts. Deletions from position -795 down to -168 had no effect on overall GUS activity, nor on the induction factor caused by elicitor treatment.

REFERENCE van de Locht U., Meier I., Hahlbrock K., Somssich I.E. A 125 bp promoter fragment is sufficient for strong elicitor-mediated gene activation in parsley. EMBO J., 1990, 9, 2945-2950.

PUBMED 2390976

END

TGP_SEQUENCE

This table accumulates information on full version of the promoter sequences and contains following fields:

SEQUENCE_ID This identifier is unique within TGP_SEQUENCE. Each SEQUENCE described is marked with genus species abbreviation, gene abbreviation, and promoter number with adding sequence abbreviation

PROMOTER_ID Cross-reference to the PROMOTER_ID in the TGP_PROMOTER table

GENE_ID Cross-reference to the GENE_ID in the TGP_GENE table

SEQUENCE Full version of the promoter sequence presented in EMBL database

END The end of the entry to the TGP_SEQUENCE

EXAMPLE:

SEQUENCE_ID Pc:PR2_P1S

PROMOTER_ID Pc:PR2_P1

GENE_ID Pc:PR2

SEQUENCE

  ggccaaga atgtatgttc atctttgatg tgccatgaag ttgaaattca atagtgtgct aattgtttaa gagttgtgtc caatagggct cctgtacaat tcaaacattg ttcaaacaag gaacctaagt tctggcaata tatataccct ctacttcatt catttttctt gcaccaaatt aagtttttgc tagctaatac aagtagtatc atcattttct tgtacataat catatacaaa gtatatatta aaattatttt tgaacgatta ttcatgggtg ctgttactac cgatgttgag gttgcatcct cagtcccagc acaaacaata tacaagggct ttcttcttga catggataac attatcccta aggttttgcc ccaggctatt aagagtatc

END

How to use TGP

To browse a list of inducers, you should perform the following:

 

On the HTML page of the TGP database you could click the hyperlink ‘TGP_PROMOTER’. This will bring up the home page of the ‘TGP_PROMOTER’ table. On the page all fields of the ‘TGP_PROMOTER’ table are listed. Click the field ‘Inducer’. On the next page you will read the description of the field. Click the button ‘List Values’ to see the list of induces of the TGP database. To find promoters responsible to elicitor treatment, click ‘elicitor’. This will bring up the list of promoters, which are induced by elicitor. Click any promoter you like.

 

The SRS system enables to make complex queries and navigation through TGP.

 

To make a query “To find promoters responsible to ethylene and elicitor treatments”, you should perform the following:

On the home page of the ‘TGP_PROMOTER’ table click the button ‘Search’.

This will bring up the Standard query form for the ‘TGP_PROMOTER’ table.

 


From the drop-down menu ‘combine searches with’, select ‘AND’ (marked by arrow 1 in the Figure).
Select the field ‘Inducer’ from the drop-down menu (arrow 2). In the text-box to the right, type ‘ethylene’ (arrow 3).
Next select the field ‘Inducer’ from the drop-down menu (arrow 2) and type ‘elicitor’ in the text-box to the right (arrow 3).
Click the button 'Submit Query' (arrow 4).

This will bring up two entries TGP_PROMOTER:Np:GN1_P1 ,  TGP_PROMOTER:At:PDF1.2_P1. Click to the entry to see the description of the promoter.

The hyperlinks GENE_ID and SEQUENCE_ID provide access to the other TGP tables. The hyperlink PUBMED provides access to PUBMED database.

 

To browse a list of keywords, presented in ‘TGP_GENE’ table, you should perform the following:

On the HTML page of the TGP database you could click the hyperlink ‘TGP_GENE’. This will bring up the home page of the ‘TGP_GENE’ table. Choose ‘Keywords’. On the next page click the button ‘List Values’ to see the list of keywords of the TGP database. Click any words you like to see the list of gene identificators. Click any hyperlink to see a gene card. 

 

By the same way you can browse a list of Products, Genes or Organisms presented in ‘TGP_GENE’ table.

In the TGP_GENE table GENE, PRODUCT, TAXON, SPECIES, KEYWORDS, ACTIVITY, GENE_ID, PROMOTER_ID and SEQUENCE_ID fields are searchable through SRS.

In the TGP_PROMOTER table INDUCER, COMMENT, SPECIFICITY, PROMOTER_ID, GENE_ID, SEQUENCE_ID fields are searchable through SRS.

It should be noted that SRS provides a possibility to view the complete list of searchable terms.

 

The typical queries to the TGP_PROMOTER table:

  • Find the promoters activated by a particular inducer (search on the fields “INDUCER” and “COMMENT”);
  • Find the tissue-specific promoters (search on the field “COMMENT”);
  • Find the promoters expressed in a particular plant species (search on the field “SPECIFICITY”).

 

The typical queries to the TGP_GENE table:

  • Find the genes activated by a particular inducer (search on the fields “KEYWORD” and “ACTIVITY”);
  • Find the genes coding a particular protein (search on the field “PRODUCT”);
  • Find the genes of a particular species presented in TGP_GENE database (search on the field “SPECIES”);
  • Find the genes of a particular species activated by a particular inducer (search on the fields “SPECIES”, “KEYWORD” and “ACTIVITY”).