Enhancer Screen

Browser Handbook

Notes:

- List of uploaded ES pages: ES_Bookmarks.html.

- A pdf version of the Browser Handbook is available for download.

- When visiting this page at low screen resolutions: clicking the Handbook's sections images will open them at their original size.

- Additional information related with the the website's design and Data Table implementation is available in Website Info.

A) Data Table

One of the most important pages of the site is the Data Table, containing all Enhancer Screen entries and allowing the users to interactively search information via filters (selectors in drop-down lists or text inputs, including operators).

Once the Data Table fully loads (it might take a while, depending of Internet speed, computer specs., operating system, browser):

• - Top Row: Number of displayed rows (1), selection of table pages (2) and number of rows per page (3). Clicking on the question mark (4) makes the Quick Help to pop-up, which contains the list of all anatomical terms used to describe the ES expression patterns. At the rightmost side there is a red cross (5): clicking on it resets all filters.


• - Second Row: contains descriptions for each column (this will be detailed below).


• - Third Row: used to filter data (text inputs or by selecting from drop-down lists).

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B) Detailed descriptions for each Data Table column

(all examples are from data on RC / v1.0 of EScreen site)

B1) ES

• This column presents the ES number attributed to each stable transgenic line generated by the EScreen.
• Filter (text input): intended ES number
• On Mouse Hover : thumbnail of the ES case
• On Mouse Click: access to the respective ES page

Reminder: visitors can click here to open a list of all ES pages included in the current version of the site; this might be handy, providing an alternative method (beyond using the Data Table) to browse the information in those pages (beyond using the Data Table).

B2) Vector

• Three different versions of the ZED vector were used in the EScreen (Tol2-LoxP-pGata-GPF, Tol2-LoxP-pZIro-GFP, ZED). The ZED vector is the most up-to-date version. For more information on these vectors please go to the "Methods & Protocols" section.
• Filter (selector): Tol2-LoxP-pGata-GFP, Tol2-LoxP-pZIro-GFP, Tol2-mCherry-pNvGata, Z48-Gw-Xcar GFP, ZED

B3) DNA Source

• In this column it is shown the DNA source used as template to amplify the enhancer regions.
• Filter (selector): Amphioxus, Human, Mouse, Nematostella, Sacogglossus, Sea urchin, Xenopus, Zebrafish

B4) Genomic Coordinates

• This column contains the coordinates of the enhancers cloned to generate the ES lines. A link is available for the genomic landscape of the corresponding ES line in the UCSC genome browser.
• Filter (text input): for example, write chr## (replacing ## by the chromosome number; note that not all links follow this standard) ;
  (hint: writing ' : ' (colon) returns a complete list of ES lines with links to UCSC)
• On mouse click: when available, link to the respective position on genome.ucsc.edu (UCSC Genome Bioinformatics). Example, ES31: hg19:chr9:22,009,390-22,012,229.

B5, B6 and B7) Expression Patterns Parameters, "Search by Anatomical Region"

• The first column (B5) describes the anatomical regions showing expression of GFP (and/or RFP) for each ES line. ES lines can be searched by expression patterns using anatomical terms. Second and third columns (B6 and B7) are available to perform searches using combination of terms. For a deeper description on how to search ES lines by anatomical terms, please see section C2.
• Filter (text input): a reference list of searchable anatomical terms is available when clicking on the question mark located at the top right side of the Data Table

B8 and B9) Paper Reference and Published Info

• Cases with published papers can be filtered by selecting 'Yes' in B9 column. If a paper has been published, its reference in B8 column is a clickable link leading to its abstract or download location. In any case, doing mouse-hover on the paper's reference may also provide additional information.
• Filter (selector, B8 column): paper's short reference (title, quick description, ID)
• Filter (selector, B9 column): paper's short reference Yes, No (published info)

B10) ZFIN Name

• In this column there is a link to ZFIN site for the published ES lines.
• Filter (selector): Drop-down list of ZFIN name.
• On mouse click: when available, gene link at zfin.org (Zebrafish International Resource Center)

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C) Data Table: Filters

Interaction with the EScreen data can be achieved by using the functionalities of the interesting HTML Table Filter Generator script that powers the Data Table.

Information can be filtered when selecting parameters from drop-down lists or when writing text inputs (and by combining such inputs with operators).

There are three operators that might be specially useful while searching EScreen's Data Table:

• =  : Exact match search, only the whole search term(s) is matched (EQUAL)
•   ! : Data that doesn't contain search term(s) is matched (NOT)
• || : Data containing at least one of the search terms is matched (OR)


• (for complete documentation please visit http://tablefilter.free.fr/doc.php)

C1) Next, a few examples about using both types of filters (selectors and text inputs):

Example1 (text input), on Genomic Coordinates:

• chr14 returns ES66, ES67 and ES68

Example2 (text input and operator), on ES:

• =ES1 exactly returns ES1 (else, if writing ES1, returns ES1, ES10 to ES19, etc)


• =ES5 || =ES29 returns both (ES5 or ES29)


• (for eventual ES equal or greater than 100 it's enough to simply write the number, without '=ES')

C2) Searching ES lines by expression pattern using anatomical terms (see B5, B6 and B7):

• Three columns are ready for text input (in order to not clutter the table, only the leftmost has visible text; the other columns are functionally equivalent though). Each column represents [AND] conditions which can be combined with operators:
• The first column (B5) describes the anatomical regions showing expression of GFP (and/or RFP) for each ES line. ES lines can be searched by expression patterns using anatomical terms. Second and third columns (B6 and B7) are available to perform searches using combination of terms.
• Filter (text input): a reference list of searchable anatomical terms is available when clicking on the question mark located at the top right side of the Data Table

Examples:

• brain, neurons, somites
  - one term in each column - (brain [AND] neurons [AND] somites) - results in ES16 (forebrain)


• forebrain, midbrain, !eye
  - results in ES1, ES8, ES11, ES25, ES39, ES45, ES46 (all without eye)


• forebrain, midbrain, eye
  - removing the '!' (not condition) results in ES13, ES48 and ES49


• forebrain, midbrain
  - results in all cases for the previous two examples

This method might not yet be very robust but it already allows a good level of interactivity: together with the filters in all the other columns it is possible to arrive at more restricted sub-groups of ES cases or at individual cases, example, ES46:

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D) ES Pages

ES pages contain additional information for each ES line distributed into three main sections: Expression patterns by anatomical domains, Images of expression patterns and Map info. They can be visited via:

• - Data Table browsing
• - Bookmarks folder (for example, created with the help of the 'ES - All Links' page.
• - Or directly, by typing the intended ES url in the web browser: http://www.upo.es/CABD/EnhancerScreen/ES/ES###.html (replacing ### by the ES number; example, 050 to access ES50.

Each ES page is divided into three main sections with extra information in relation to what is visible in the Data Table.

D1) Expression patterns by anatomical domains:

• The GFP (and RFP, if available) expression is annotated by anatomical domains, corresponding to a developmental times that span from 24 to 60 hours post fertilization (hpf).
• In the data table (B5), these anatomical domains are concatenated and GFP and RFP expression is not discriminated.

D2) Images of expression patterns:

• If available, thumbnails are provided for the individual channels (GFP or RFP) for 24 to 36 and 48 to 60 (hpf).
• Higher resolution versions of these images can be viewed if clicking in each thumbnail.

Note: the 'thumbnail' size is dynamically dependent of monitor / web browser resolution (if using modern browsers).

D3) Map Info

• Primer F and R sequences used to amplify the enhancer regions.

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E) References

1. Zebrafish Enhancer Detection (ZED) Vector: A New Tool to Facilitate Transgenesis and the Functional Analysis of cis-Regulatory Regions in Zebrafish.

José Bessa, Juan J. Tena, Elisa de la Calle-Mustienes, Ana Fernández-Miñán, Silvia Naranjo, Almudena Fernández, Lluis Montoliu, Altuna Akalin, Boris Lenhard, Fernando Casares, and José Luis Gómez-Skarmeta.

DEVELOPMENTAL DYNAMICS 238:2409–2417, 2009