GeneSeeker help pages




About this help

This Help window contains descriptions of the terms used in the interface and a step-by-step example to guide you through GeneSeeker options. All help information is in this window.



Genetic location:

Fill in a genetic location by specifying chromosome, arm and band. To specify a range, separate the two locations with a hyphen, e.g. 7p15-7p21 (example 1).
Chromosome values can be numbers, X, Y or Mt. Arm values can be p or q. Band values can be numbers or cen for centromere, ter for terminal. Combinations can be made, using the logical operators such as AND, OR and NOT (example 2).

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Example 1: Basic format for the genetic location.

Example 2: Combining different genetic locations.




Exclude genetic database

A genetic database can be excluded from the search. Choose MGD, MIMMAP or GDB: when MGD is selected, the Oxford-grid is also excluded.

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Expression location

A tissue of interest or a phenotypic feature of a syndrome can be specified. If the genetic location is not specified, the script will only search for expresion locations. Wildcards (*) are allowed, but keep in mind that not all databases support this option. Combinations can be made, using logical operators such as AND, OR, and NOT, e.g. brain NOT liver. There is no limit on the number of tissues specified.

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Example 1: Expression localisations/tissues can be combined by Boolean operators.


Example 2: Braces and Boolean operators.

Example 3: Double terms like "upper limb" must be enclosed in double quotation marks.




Exclude expression database

Here an expression database is excluded from the search. Either choose from MEDLINE , SWISSPROT-TREMBL (UniProt) , TBASE* , GXD or OMIM.

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* TBASE contents are merged with the Mouse Genome Informatics database. We use the phenotype information from the MGI database in searches.



Max. distance oxford-grid

The Oxford-grid converts human genetic localizations to mouse localizations (a chromosomal range in cM), in order to be able to search mouse gene localization databases. This conversion is done dynamically by searching for human genes at the specified locale and retrieving the corresponding mouse homologues. The determined localizations of these mouse genes are used to create a list of syntenic mouse regions. This is done by treating two gene localizations as one range if these genes are separated by less then a certain treshold: Max. distance Oxford grid (in cM).

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Exclude Housekeeping genes

When this box is checked, housekeeping genes obtained from SWISSPROT (UniProt) are excluded.

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Other genes to exclude

Genes to be excluded can be specified here.

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Thesaurus of search terms

This thesaurus can be used to enter search terms into the expression input field. (based on: van Steensel MA et al. (1999) Probing the gene expression database for candidate genes. Eur.J.Hum.Genet. 7 (8):910-919.)

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Example 1: Selecting eyes in the "Thesaurus-category" will copy the terms into the expression location field. Combinations of Thesaurus categories can be made using the copy/paste function of your browser.




Thesaurus-category

These are the main categories of the thesaurus, if one category is selected the search and embryology terms are displayed. The search terms are all copied to the expression input field and combined with OR operators (see thesaurus).

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Search term

These are the search terms belonging to each of the categories. Upon selection, the term is copied to the expression input field (see thesaurus).

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Embryology term

These are the embryology terms belonging to each of the categories. Upon selection, the term is copied to the expression input field (see thesaurus).

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Use embryology terms

If this option is checked, the embryology terms are also copied to the expression input field when a category is selected (see thesaurus).

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Zuerich genetic locations

The zuerich list can be used to enter search terms into the genetic input field. The genetic regions are based upon malformations caused by deletions of entire bands. (based on: Brewer C. et al. (1999) A chromosomal duplication map of malformations: regions of suspected haplo- and triplolethality--and tolerance of segmental aneuploidy-- in humans. Am.J.Hum. Genet. 64 (6):1702-1708. and Brewer C. et al. (1998) A chromosomal deletion map of human malformations. Am.J.Hum.Genet. 63 (4):1153-1159.)

Example 1: Selection of "craniofacial" abnormalities, and subsequently "cleft palate" shows the genetic location hints for the Zuerich dataset.

Example 2: Since the "Paste 'high significant bands'" option is set (bottom of the example 1), the location hints are copied to the search field.



Zuerich-category

These are the main categories, upon selection the malformation belonging to the category are shown (see zuerich).

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Malformation

These are the malformations: upon selection the low-significant associated bands and the high-significant associated bands are shown. Either the high- or low-significant associated bands are copied to the genetic input field, in accordance with the selection made (see zuerich).

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Low-significance bands

These are the associated bands with a significance of P < 0.05 (see zuerich).

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High-significance bands

These are the associated bands with a significance of P < 0.001 (see zuerich).

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List of queries to submit to batch

When a large number of GeneSeeker queries are to be run, it is better to use a queueing system than to submit all the queries simultaneously. The batch/queue will register your requests and run the jobs when there is enough room on the machine. Make sure to fill in your email address correctly, as a hyperlink to the results will be returned by email.

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Example 1: Click the "add to batch list" button to add this query to the batch-list (see example 2).

Example 2: The query has be added to the list (see example 1). Make sure to fill in your email address correctly, as a hyperlink to the results will be returned by email. Other queries can be added as well, as is shown in example 3.

Example 3: Two queries, one to search "eye AND ear", and the other to search "eye OR ear", are in the batch list. Manual editing this list is possible, but remember that the queries are separated with "%@%".




Step-by-step example run

Step 1:

A GeneSeeker analysis on Trismus-Pseudocamptodactyly syndrome (TPC; MIM 158300). This syndrome has been linked to 17p12-p13.1*. TPC is characterized by defects in muscle tissue mainly in limb and/or mouth. The query can be formulated as: "17p12-p13.1 / (limb OR mouth) AND muscle". The default Max. Oxford-grid distance is correct in most occassions. Clicking on the "Search" button starts the query.

*) Veugelers, M., Bressan, M., McDermott, D.A., Weremowicz, S., Morton, C.C., Mabry, C.C., Lefaivre, J.F., Zunamon, A., Destree, A., Chaudron, J.M. et al. (2004) Mutation of perinatal myosin heavy chain associated with a Carney complex variant. N Engl J Med, 351, 460-469.

Step 2:

A new webpage is opened, showing the progress of the search and the results. All databases that are searched are shown with the submitted query. Notice that the GeneSeeker is still running (here by the 2 arrow at the upper left corner, in front of "Your search result"): don't press the stop button of your browser. The link "limb_17p12-17p13.1_40501" points to your search results if you want to access them later. This link will be active for 14 days.

Step 3:

During the GeneSeeker run you are informed of completed queries, e.g.: "Subquery finished: medline express muscle". When all queries finished, the results per database are summarized (here e.g.: "Genes retrieved from omim, query limb: 328"). Clicking the links will show you the raw datbase web-page results. Notice that GeneSeeker is still running and filtering the results: don't press the stop button of your browser.

Step 4:

Notice that generating the tables can take a minute, so don't stop the run until your browser reports: "Done" at the bottom of the window, or your browser logo animation on the top right has stopped.

It has been shown that mutations in the MYH8 gene can cause Trismus-Pseudocamptodactyly syndrome*. All results are now divided over four tables.:

*) Veugelers, M., Bressan, M., McDermott, D.A., Weremowicz, S., Morton, C.C., Mabry, C.C., Lefaivre, J.F., Zunamon, A., Destree, A., Chaudron, J.M. et al. (2004) Mutation of perinatal myosin heavy chain associated with a Carney complex variant. N Engl J Med, 351, 460-469.





Updated: March 25, 2005