Site map

within PAREO Web interface, the navigation bar is always present at the top left of the page, just below PAREO's logo. It provides quick links to the main PAREO functions.
First to the left, Home page link, which redirects to the search page (see Searches).
Then links to the hierarchically treeviews used to browse through Pathways, Enzymes, Compounds and Species classification.


Classification :

In theses pages, data is hierarchically organised. Each line correspond to one single item, which may have children items (i.e. data from the level immediately below). The line can be subdivided in (at most) 3 parts :
  1. starting from the left side, there is a navigation sign (+ or -) which serves to expand or collapse the view of the children items.
  2. an optional item id, which redirects to a page describing the corresponding item in details (Enzyme, Compound), or to a page which displays the Pathway map.
  3. Finally, the complete name of the item.
Note that :


Species classification :

It basically resembles to the classification pages described above, except that each line contains a check box which is used to create group of species. This is done in a two steps procedure :
  1. check species to be associated within a group,
  2. click on the "add to new group button".

Every group that have been created are displayed on the right side of the page.
Clicking on the "Edit group" button, redirect to a specific page which allow to set a meaningful name to the groups, remove some species from groups, or even to delete a whole group (see Edit group).

Remember that : By clicking on the "Edit fictive species" button, it is possible to create user defined species with its associated enzymes and use it as any other species (see Edit fictive species).


Edit groups :

Groups of species (created in the species classification page) are used to perform pathway comparison.
This page display all groups defined by the user, and allow to perform one edit operation at a time.

instructions : Note : groups are stored in a cookie within the web browser.


Edit fictive species :

It is possible to create Fictive species for species which are not included in PAREO database.
Basically, it allows to associate a list of EC number to a name.
Then, the Fictive species may be used as any others species, for example in map colouration or gene list, or even to create group of species.

instructions :
  1. click on the "Add new fictive species" button (a new block appears in the page)
  2. Enter the list of EC (one by line) in the text area of the block corresponding to the new fictive species.
  3. click on the "Apply change to EC list

One name and one url may be added besides each EC number (fields are separated by a white space). The name will appears in gene lists (instead of EC number). The URL will be used in hyperlink in the pages where the name appears.

Note : fictive species are data private to the browser session.


Pathway map (Metabolism comparison):

This page display the image of the selected pathway.
The image may be coloured to display conserved parts of metabolic pathways among different species.

instructions : Select one or more species or groups, then click on the "display" button.
(use [Ctrl]+click to select several lines in species/groups lists)

interpretation : Like a checkboard, each box corresponding to an enzyme is divised in small zones (one for each selected species). These zones are individually coloured in accordance with the fact that there is a gene corresponding to the enzyme in the respective species genome.

Map colouration may be also performed by groups of species by clicking on the "Display by group" button.
In this case, the saturation of the color used is variable, in proportion to the number of species of the group having a gene corresponding to the enzyme.

Most elements of the image are active. It means that a popup information window appears when the mouse cursor flies over a specific element. It is also possible to click on most active elements to get detailed information about it.

Tip : PAREO remembers the last selection of groups or of species, and use it whenever a new pathway is displayed.
Reference Pathway image (without any colouration) may be obtained by selecting "Reference Pathway" in the species list.


Searches :

instructions : Type one search term into the text box, and click on the "Search" button to retrieve search results.
Searches are not case sensitive, and the text entered is searched in names, ids and synonyms (and definitions for genes)

It is possible to perform searches with partial term, by using special character % (percent) which matches any character string.
For example, search for enzyme with query "1.16.%" will retrieve all enzymes whose EC number starts with "1.16.", i.e. the Oxidoreductases oxidizing metal ions.


Gene list by pathways and by species :

instructions : Select one or more pathway and one or more species, then click on the "Search" button.
(use [Ctrl]+click to select several lines in pathway or species/groups lists)

The results are grouped by pathway, and displayed in a table where each row corresponds to an enzyme described in the pathway.
Tip : It is possible to export the table in a tab delimited format (to import in your favorite spreadsheet software) by clicking on the [export] link located in the top left cell off the table.


Find pathway by EC:

instructions : Type a list of EC number in the text box, and click on the "Search" button.

A table is displayed with all the pathways containing at least one of the EC entered.
Tip : partial EC number, like 3.1.2.-, can be used here.