Expression Disruption Screen

Browser Handbook

Notes:

- List of uploaded ED pages: ED_Bookmarks.html.

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

- 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 Expression Disruption 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 in the question mark (4) makes the Quick Help to pop-up, which contains the list of all anatomical terms used to describe the ED 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 selecting from drop-down lists).

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B) Detailed descriptions for each Data Table column

(all examples are from data on v1.0 of EDscreen site)

B1) ED

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

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

B2) Construct

• Four different versions of the ED vector were used in the ED screen (IIC, IMP16, IMP17 and IMPCherry). Most of the ED lines were generated using the IIC vector which is the most up-to-date version of ED. For more information on these vectors please go to the "Methods & Protocols" section.
• Filter (selector): IIC, IMP16, IMP17, IMPCherry, n.a. (not available)

B3 and B4) GFP and RFP Expression

• In these columns the presence or absence of GFP and RFP expression is discriminated for each ED line.
• Filter (selector): + (expression), - (no expression)

B5) GFP vs RFP Expression

• In this column is indicated if the GFP and RFP expression patterns are similar or different for each ED line.
• Filter (selector): Only GFP, GFP ~ RFP (Similar), GFP ≠ RFP (Different)

B6) Map

• This column contains the coordinates of the mapped ED lines. These coordinates correspond to the Jul. 2010 zebrafish (Danio rerio) Zv9 assembly. Also, a link is available for the genomic landscape of the corresponding ED line in a shared session in the UCSC genome browser. Here you will find a track indicating the exact insertion point of ED, with its corresponding orientation, either GFP RFP or RFP GFP oriented (see example below). Other useful tracks are also available, as the enhancer associated epigenetic marks H3K4me1 and H3K27Ac and the promoter associated epigenetic mark H3K4me3 at different developmental times (Bogdanovic et al., 2012).
• Filter (text input): write chr## (replacing ## by the chromosome number; note that not all links follow this standard, example: ED46, ED54)
  (hint: writing ' : ' (colon) returns a complete list of ED lines with links to UCSC)
• On mouse click: when available, link to the respective position on genome.ucsc.edu (UCSC Genome Bioinformatics). Example, ED198: chr15:32792486-32992495.

B7) Associated Gene

• After mapping the insertion point of an ED line, the expression patterns of nearby genes were compared to GFP and RFP expression. When nearby genes show similar expression patterns to the reporter genes (GFP and/or RFP), that ED line is considered to be associated to that gene. In this column the identified associated gene is annotated. In addition, a link to the gene web page in the zfin site is available.
• Filter (selector): Drop-down list of associated genes
• On mouse click: when available, gene link at zfin.org (Zebrafish International Resource Center)

B8) Mutant

• This column discriminates if an ED line is mutant or not. This was accessed by performing in situ hybridization or qPCR for the associated gene in 24hpf embryos from an incross of the corresponding ED line. When a decrease in the levels of the transcript are detected, the ED lie is considered mutant and annotated in this column.
• Filter (selector): Yes, No, n.a. (not available)

B9, B10 and B11) Expression Patterns Parameters, "Search by Anatomical Region"

• The first column (B9) describes the anatomical regions showing expression of GFP and/or RFP for each ED line. ED lines can be searched by expression patterns using anatomical terms. Second and third columns (B10 and B11) are available to perform searches using combination of terms. For a deeper description on how to search ED lines by anatomical terms, see section C2.
• Filter (text input): a reference list of searchable anatomical terms is available when clicking in the question mark located at the top right side of the Data Table

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C) Data Table: Filters

Interaction with the EDscreen 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 EDscreen'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 Map:

• chr15 returns ED16, ED20, ED21, ED33, ED155, ED191, ED198

Example2 (text input and operator), on ED:

• =ED8 exactly returns ED8 (else, if writing ED8, returns ED8, ED80, ED81, etc)


• =ED5 || =ED29 returns both (ED5 or ED29)


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

C2) Searching ED lines by expression pattern using anatomical terms (see B9, B10, B11):

• 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 (B9) describes the anatomical regions showing expression of GFP and/or RFP for each ED line. ED lines can be searched by expression patterns using anatomical terms. Second and third columns (B10 and B11) are available to perform searches using combination of terms. For a deeper description on how to search ED lines by anatomical terms, see section D2.
• Filter (text input): a reference list of searchable anatomical terms is available when clicking in the question mark located at the top right side of the Data Table

Examples:

• brain, eye, fin
  - one term in each column - (brain [AND] eye [AND] fin) - results in ED5 (Midbrain)


• forebrain, notochord, !eye
  - results in ED62A, ED82, ED84, ED104, ED105, ED131, ED185, ED215


• forebrain, notochord, eye
  - removing the '!' (not condition) results in ED66 and ED196


• forebrain, notochord
  - results in all the previous two cases

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 ED cases or at individual cases, example, ED239:

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D) ED Pages

ED pages contain detailed information for each ED line distributed into three main sections: Expression patterns by anatomical domains, Images of expression patterns and Map info.

• - Data Table browsing
• - Bookmarks folder (for example, created with the help of the 'ED - All Links' page.
• - Or directly, by typing the intended ED url in the web browser: http://www.upo.es/EDscreen/ED/ED#####.html (replacing ##### by the ED number; example, 00155 to access ED155.

Each ED 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 expression is annotated by anatomical domains, corresponding to a developmental times that span fro 24 to 60 hours post fertilization (hpf).
• In the data table (C9), these anatomical domains are concatenated and GFP and RFP expression is not discriminated.
• In the Data table, the GFP Exp, RFP Exp (C3, C4) and GFP vs RFP (C5) columns are relative to the contents of this Expression table.

D2) Images of expression patterns:

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

Note: thumbnail's size is dynamically dependent of monitor / web browser resolution (if using non-discontinued browsers).

D3) Map Info

• When information about the ED insertion point is available, a sequence containing the transposon (at bold) and the contiguous genomic sequence will be displayed. Sequences were obtained by performing inverse PCR for the "GFP side" or "RFP side" tip of the transposon.
• Sequences from each side of the transposon (GFP or RFP side) can appear more than once and correspond to results obtained by independent rounds of inverse PCR.

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E) References

1. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Bogdanovic, O., Fernandez-Minan, A., Tena, J. J., de Lacalle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S. J., Veenstra, G. J. C., and Gomez-Skarmeta, J. L.

Genome research (2012)