TRANSPATH® Professional SEARCH ENGINE
 

Quick Search


The search engine should enable you to search and browse the TRANSPATH database. By default, it will also query NetPro™ data (if licensed).This opportunity can be switched off. The basic search and retrieve function is a very easy one. First, choose the table you are interested in using the menu on the left. This will open the main search form.


Fig.1 Molecule Search Form

Enter the terms with which you want to query TRANSPATH in the input boxes on the left. Here you can connect up to three search terms with the logical operators AND, OR, or NOT. Wildcards are set automatically in front of and behind every search term. For searching with lists of search terms (e.g. gene lists from microarray experiments) please fill into the top input box on the left and use a new line for every search term you have. You can also upload a text file with your search items.

Now choose the appropriate search fields in the lists in the middle, called Quick Search Fields. These lists show all field names that occur on the data sheets for the corresponding table.
You can specify the columns you want to appear in the result list by selecting fields in the list box (Output fields) on the right. Choose multiple output fields by holding the STRG/CTRL key while clicking. Press the help button below the list field to find out more about the meaning of each field name. After you have made your choice, click on the Submit Query button and the query will start.
Example 1 In this example we want to find all reactions in which the G-protein Ras is involved.
We click on REACTION and enter Ras as the search term and choose Name as the Quick Search Field.
The result will be a long list of entries (This example output list is not operable).
 

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Extended Search


The extended search function allows you to save your query and combine it with an unlimited number of other queries using logical operators.
To identify your query on the web server enter a name in the field Name for your search. Check the field NEW below the list of search fields (it is checked by default). By submitting the query, it is automatically saved.
To combine one query with another one, open the search form again by clicking on Molecule or Reaction in the menu bar (please do not use the back button of your browser). Open the pull-down list Select a previous search you want to refine and select your previously saved query. If you have not specified a name for your query you can select last search for your latest search.
Enter the query you want to use for combination and select one of the logical operators on the right. The possible combinations are:
NEW Start a new search
AND AND will reduce the result by an additional criterion.
In our example, Ras AND semantic will give us all reaction entries that belong to both categories, e.g. all semantic entries concerning Ras.
NOT NOT will reduce your result set as shown in example 2.
OR OR will increase the result by adding a second category.
A query for Ras OR PI3K will result in all entries either with Ras or with PI3K.

In this manner you can save and combine as many queries as you like.
The stored queries can be opened for viewing and working at any time.


Example 2 We run the same query as in example 1, but enter ras_search as the name for the query.
After getting the same result as before, we start another query by clicking on REACTION again.
Now we enter mechanistic as the search term and Type as the search field.
After that we choose the query ras_search instead of last.search and check the checkbox NOT.
If we submit the query, the search engine will perform a "reactions with Ras but NOT mechanistic" query.
Looking at the result, the mechanistic reactions are gone.
 
In addition to the automatically set wildcards in front of and behind your search term, a number of special characters (which are metacharacters of Perl regular expressions) can be used to confine your search results.
 
Metacharacter Example
. replaces any single character Cdk.(h) as a search term finds all human Cdks (Cdk1(h), Cdk2(h),...).
[...] defines a class of characters that are allowed at this position trans[ac] finds transactivation or transcription, but not transregulation
[^...] defines a class of characters that are not allowed at this position STAT[^3-6] retrieves only STAT1 and STAT2, but not STAT3, STAT4, STAT5, and STAT6
* quantifier, allows none or any number of the preceding character trans.*activator retrieves 'transcriptional activator', 'trans-activator', and 'transcription activator'
^ stands for the beginning of a line ^Smith finds all references with a first author named Smith
\character "masks" character if it is a metacharacter, so that it can be used as a "normal" character in the search term. Cdk1\(h\)
 
 

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Search for pathways with a list of molecules


This search function should be applied when you have a list of molecules and you want to find out which pathways they are involved in. The mapping of your list to the canonical pathways in the pathway flatfile is a two-step procedure:

  1. The list of molecules can be represented by unique names (eg. HGNC) or a list of identifiers from the public databases LocusLink, Unigene, SWISS-PROT, or EMBL/Genbank/DDBJ or by Affymetrix array probe set IDs. Each name or identifier should be in a separate line. Copy and paste the list in the search term field of the molecule search engine or upload it as a file. Select molecule name or external database hyperlinks (depending on the kind of identifier you use) from the search field list and start the query.
  2. The search result list shows all matched entries in TRANSPATH®, which are species-specific and have the type basic. As the pathway entries are made up of abstracted molecule entries (species-unspecific and sometimes groups of isoforms or splice variants), complexes, and modified forms, it is necessary to retrieve a list of abstracted molecule entries, complexes, and modified forms that corresponds to the basic molecule list. For doing this click on the Start pathway search link on top of the basic molecule list.
    The result is a list of pathways in which at least one of the listed molecules has been found. Each pathway entry lists all matched molecules. You can visualize a pathway by clicking on Quick network view. The molecules in the pathway map that match to your original molecule list are highlighted in blue.

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Further Query Examples


When you are looking for disease-related molecules and their signaling behavior, use comments as the search field. You will get the best results, if you enter one of the keywords which cover a broad range of the most common diseases.


Example 3 To find all human molecules with an annotation containing the keyword inflammation,
we can run a query with this keyword as the search term and comments as the search field.
We have to combine this query with a second search (term: human, field: Organism species) using the AND operator.
 
If you are interested in which molecules reside in a certain subcellular compartment, use location positive as the search field. TRANSPATH® uses the same vocabulary for subcellular structures as the ontology cellular compartment from the Gene OntologyTM Consortium (you can find several browsers for this ontology on the website).
 

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Query Analyzer


An example of how you can analyze your query result lists for common molecules or reactions in the vicinity of the signaling network is described in detail for gene expression array data and the ArrayAnalyzerTM. This functionality allows you to cluster molecules or reactions and to identify possible key nodes in signaling networks.

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