Introduction

Thea-online is a knowledge base dedicated to humain genes. It integrates information from the following sources:

UniProt,
Intact,
GOA,
Ensembl,
Gene Ontology,
NCBI
KEGG

How to perform a search in Thea-online

Search in Thea-online has been designed to be as simple as possible. You don't need to format your queries in a special way or to specify th e name of the database your query identifier comes from. Simply type or paste in the text area the name, symbol, alias or identifier of the ge ne or gene product you are interested in to obtain detailed information of it in your browser window. Most of the identifiers currently in use unambiguously identify a unique gene. When a same identifier can be matched to several genes, a message ask you to choose in a list of possib le matches

For example, the string 120534 corresponds to kegg id 120534 and ncbi gene id 120534, identifying the gene C11orf46 chromosome 11 open reading frame 46 but also matches identifier 120534 of GDB corresponding to gene ACACA.(try to search Th ea-store for 120534)

Example of searches

Try the following searches with Thea-online :

The gene label brca1
The aliases dhtr or nr3c4 of gene androgen receptor,
The full name Cyclin-dependent kinase 6 inhibitor,
NCBI's GI 11386203,
Uniprot's accession number O43929,
OMIM entry 607387,
CCDS14617 from CCDS database,
EMBL's accession number AJ222657,
NM_181741 from RefSeq,
Affymetrix's probe id 206290_s_at.

Search results

Information displayed as the result of a search is divided in several sections : Gene Description, General Informations, Interactions, Probes, Pathways, Annotations, Citations. To limit the amount of data displayed, it is possible to select the type of information displayed by using the options panel.

As an example, we detail below the results of a query done with the search term fancd1

Gene Description

This section display some general information about the biological object detailed in the page. This allows to quickly check if the report corresponds to the gene or gene product we are interested in

Searched string=fancd1, label of up:P51587 which corresponds to the following entry

gene: breast cancer 2, early onset, BRCA2 (breast cancer 2, early onset)

type: protein coding

The firt line is an explanation of the database entry that matched the searched term. In our example, fancd1 matched the label of the protein identified by the entry P51587. The second line displays the standard name and description (BRCA2, breast cancer 2, early onset) of the gene encoding this protein. The third line if the type of the biological object ; protein coding in our example

General Informations

Four type of information is available in this section

Gene and Gene products

A graphical representation of the gene and its transcripts and translations is displayed. This information is extracted from the ensembl database and links to this database entries are provided.

Aliases and Descriptions

Names and descriptions of the entry, used in several databases is provided here. The origin of the information is displayed as well. In the following list, we can see that FANCD1 is a label used in Uniprot (symbol uniprot ) while BRCA2 is used in both Uniprot and Ensembl (symbol ensembl ).

Breast cancer type 2 susceptibility protein
BRCA2 ,
Fanconi anemia group D1 protein
FANCD1
breast cancer 2, early onset

Other identifiers

This section displays identifiers related to this entry in other databases.Gene, Transcript and Translation categories contains equivalent biological entries. Identifiers in other databases that are related to the current entry but not strictly equivalent are grouped in the category Undetermined.

Genomic location

This section displays the chromosomal position of the displayed gene

Chromosome: 13

Start position: 31787617

End position: 31871806

Strand: 1

Cytogenetic band: q13.1

Interactions

Gene interactions are displayed in the following form :

ncbi-geneid:10362 PMID:11207365
ncbi-geneid:5888 , ^Intact ,PMID:15800615 PMID:9126738,12619154 PMID:9774970
ncbi-geneid:7979 PMID:10373512,12228710
ncbi-geneid:8850 PMID:9824164
up:P60896 , ^Intact
...

Each entry represents an interactor of the gene. By default, the NCBI gene id is used as the identifier of the interactor. Source of the information is displayed (for example uniprot for Uniprot, ncbi for NCBI and ^Intact for Intact. When available, a reference to a PubMed entry describing the interaction.

Probes

The list of probes hybridizing a transcript of the gene with a reference to the database in which this information was retrieved.

Pathways

The list of metabolic pathways for the gene with a reference to the source database ( kegg for Kegg).

Annotations

Annotations of the gene products with the evidence code supporting the annotation and a reference to the source database ( ensembl for Ensembl, uniprot for Uniprot and ^GOA for GOA). Annotations displayed here are Gene Ontology terms and SwissProt keyword. In the case where there is equivalence between these two terms, GO terms are preferred.

GO:0000074 regulation of progression through cell cycle TAS ^GOA , ,
GO:0006281 DNA repair ,IEA ^GOA ,
GO:0005615 extracellular space TAS ^GOA , ,
GO:0016563 transcriptional activator activity IDA ^GOA
SwissProt Keyword:225 Disease mutation
GO:0005737 cytoplasm IEA
GO:0007093 mitotic checkpoint NAS ^GOA , ,
GO:0003697 single-stranded DNA binding NAS ^GOA , ,
GO:0005634 nucleus IDA ^GOA , ,
SwissProt Keyword:677 Repeat
GO:0005515 protein binding IPI ^GOA , ,
SwissProt Keyword:621 Polymorphism
GO:0045449 regulation of transcription TAS ^GOA , ,

Citations

The list of citations related to the current entry with a reference to the source database ( uniprot for Uniprot and ncbi for NCBI). When a supplementary description is associated, it is displayed before the source database.

PMID:12442273,VARIANTS ASP-1593 AND SER-2706 Two BRCA2 missense variants were identified in breast cancer patients in India.
PMID:12915460
PMID:15314155,Results suggest that BRCA2 expression levels are regulated by ubiquitination in response to DNA damage and that USP11 participates in DNA damage repair functions within the BRCA2 pathway independently of BRCA2 deubiquitination.
PMID:16731627
PMID:15319244,Patients with bilateral breast cancer having BRCA2 mutations are significantly younger than non-carriers.

Customizing the display page

The Option menu, displayed on each page, is a link to a parameter page allowing and easy configuration of the search.

Type of information allows to choose the categories of information to display on the result page
Sources of informations allows to select if we want the origin of information displayed on the result page and to choose the sources that has to be collected.

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