Genatlas help

Founded in 1986, GENATLAS compiles the information relevant to the mapping efforts of the Human Genome Project. At this day ( 15/01/2010), this information is collected from more than 82481 articles in the literature, collected in more than 870 reviews. The articles are daily analyzed by annotators to update the GENATLAS database. Only the objects with a known cytogenetic location are retained.

number of articles By reviews

GENATLAS repertories three kinds of objects

- Genes database ( more than 22.431 entries)

- Phenotypes database ( 4350 entries)

- References database linked to the two previous ( more than 82000 entries)

I) How to query GENATLAS ?

The three databases may by queried in full text mode. You enter one or more terms separated by a blank, and all the sheets containing those terms will be displayed. When term’s length is over 3 characters, right truncature is assumed ( ie cytogenet for cytogenetic). Dash characters ( - ), if present are optional.

II) Specific GENES database query

A recent effort of the genatlas team was to format the gene object in more than 400 items, to provide a real multicriteria mode of query, more specific than the full text search mode.

The gene record is divided in 6 chapters :

- General informations

- DNA informations

- RNA informations

- Expression and localization informations

- Proteins informations

- Pathology informations

For each chapter, we supply a query screen with the concerned items. At last a query screen combining all chapters (all sections) provide the possibilities to query the genes databases on all items. When more than one item is provided, the query is an intersection ( ie AND ).

5 types of item are proposed

Free box location

You type a relevant keyword to the item. (ie for location : 9q to query all genes on 9q arm). Right truncature is assumed.

List of value ( thesaurus) protein category adaptor adhesion antigen antioncogene chaperone/stress DNA associated enzyme immunity/defense motor/contractile protooncogene receptor receptor nuclear receptor membrane regulatory secretory RNA associated signaling sign. hormone sign. neurotransmitter sign. cytokine sign. growth factor storage structural protein transcription factor transport transport carrier transport channel unknown/unspecified click here to view an example

You may choose a value in the list (ie choose adaptor to query all adaptor genes)

Check box precursor

Click the box to query all the genes coding for a protein with a precursor

Check box associated with a free box interaction    DNA RNA Protein

Choose the kind of interaction and type a term in the free box (right truncature is assumed)

Tree Thesaurus    Protein - Cellular and physiological process click here to view an example

Click the to obtain the window with the tree thesaurus. Choose a value and click the Valider button. Do not forget to close the tree thesaurus window.

After having choosen your values, click the FIND button and the query is submitted. The founded sheets will be displayed on a tabular form. Click a symbol to view detailed sheet.