eFP-Seq Browser

Welcome to the eFP-Seq Browser! Click on any of the following collapsing cards to learn more about how the eFP-Seq Browser works and how you can use it.

The eFP-Seq Browser allows you to explore RNA-seq-based gene expression levels for your gene of interest in different expression datasets. Simply enter your gene identifier in the first box on the left, select a dataset, adjust the options if desired, and click Load Data. The output is a table depicting your gene’s expression details (readmap coverage, RPKM expression levels) across all the samples in the database. Try it with the default settings!

The navigation bar has multiple options which allow you to control and manipulate the information that will be visualized in the eFP-Seq Browser.

Gene name/AGI ID

The first option is choosing your locus/gene by inserting its related AGI ID. Our autofill option can sometimes match protein names with certain genes so if you do not know your desired AGI ID (example AT2G24270), you can search by protein name.

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Dataset

By default, two public datasets will be available which will be the 113 RNA-seq data sets used by Cheng et al. to reannotate the Arabidopsis genome for the Araport 11 build (https://dx.doi.org/10.1111/tpj.13415), labelled "Araport 11 RNA-seq data" and Klepikova et al.’s Development Map (https://dx.doi.org/10.1111/tpj.13312), labelled "Developmental transcriptome - Klepikova et al".

Once a dataset has been uploaded, a new option will be present called "Uploaded dataset" which will hold the last uploaded dataset to the eFP-Seq Browser. To see how to upload your own files, check out the "Visualize your own data" help card or "XML Parameters" help card.

There will also be the option store your uploaded datasets onto your account which utilizes Google. Just click the login button on the bottom left to login and whenever you upload a dataset and select it to be uploaded to your private account, it will now be stored to your account. If you wish to delete any XMLs, you can just click the "Manage Account" button. You can learn more on the "Manage Person Account" help card.

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RPKM mode

RPKM (Reads Per Kilobase per Million reads mapped) mode has two options to chose from:

Absolute:

Absolute displays the calculated RPKM values for all visualized mapped RNA-Seq datasets. RPKM is calculated and used to normalize the effects of the length of a gene and the size of the cDNA library. By computing these values, the number of reads mapped is normalized to the length of the gene in kilobases and to the number of reads mapped in the entire experiment in mega bases.

Relative:

Relative displays the log2 of the RPKM compared against its average. In relative mode, the RPKM values of the appropriate control experiment or experiments are used to compute the fold-change in expression (increase or decrease) of the gene in question in that sample relative to the control (if no control is apparent, we use the average expression level for that gene across all samples in an experiment). Relative attempts to display all RPKM values between a scale of -5.0 to +5.0.

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Y-axis scale

The "Y-axis Scale" input option changes maximum displayed y-axis for the mapped RNA-Seq information. The default is set to auto which will have each individually mapped image have their own y-axis set to its own maximum while if a manual input value is inserted, then all images will have that maximum input.

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Absolute max

The absolute max value represents what the possible maximum RPKM can be visually represented as within the eFP images.

NOTE:

This value automatically changes whenever you click "Load Data". To update this value, simply start typing into the input box AFTER the data has been loaded.

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Load data

Once all settings have been determined (you can leave some or all to default), you can click "Load Data" to begin to visualize your data on the eFP-Seq Browser.

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Hide/Open navigation bar

It may be helpful to note that you can hide (and open) the navigation bar by clicking on the menu icon on the top left of the screen.

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The eFP-Seq Browser consists of multiple additional features that you may use to enhance your experience. This help card will go over the "eFP Overview" and "Download table as CSV". If you wish to learn more about Account management, see the "Manage Person Account" help card or if you wish to learn more about visualizing your own data ("Generate Data" and "Upload Data"), please check out the "Visualize your own data" help card.

eFP Overview

The eFP Overview is a feature that allows you to see a visual table of all the coloured eFP images for the visualized data. This information will be responsive to any filtered changes made to the RNA-Seq table.

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At the top of each eFP Overview modal displays the following information:

AGI-ID Link	This links to an Arabidopsis.org page for more information about the locus that has been queried for
eFP Colour Scale	Show what the colours of each image represent
Min and Max RPKM	Minimum and maximum possible RPKM for the chosen RPKM mode

Hovering over each individual eFP image also gives the title for the relevant eFP.

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Clicking on an eFP image will also send you to the datapoint within the RNA-Seq table.

Help image for clicking an eFP image sending you to the corresponding RNA-Seq table row

You can also click on the small camera icon in the top right-hand corner of the module to download the eFP Overview as an image. To see how this work, scroll down to the section on "Download table as an image".

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Download table as CSV

This feature allows you to download the current RNA-Seq table as a CSV file which can be opened with Microsoft Excel and Google Sheets. The CSV consists of the following columns:

Column name	Column description
Title	The given title for each individual BAM entry/file
Record Number	The SRA/SRR record number/identifier for the individual BAM entry/file
Tissue	The tissue the data in the BAM entry/file corresponds to (for a list of readable names in the eFP-Seq Browser, please see the "XML Parameters" help card)
Tissue subunit	The subunit of the selected tissue the data in the BAM entry/file corresponds to (for a list of readable names in the eFP-Seq Browser, please see the "XML Parameters" help card)
Locus	The gene region that is being queried
bp Length	The basepair length of the queried locus in the BAM entry/file
bp Start site	The basepair start location of the queried locus in the BAM entry/file
bp End site	The basepair end location of the queried locus in the BAM entry/file
Total number of reads	The total number of reads in the BAM entry/file. A read refers to a sequence of base pair(s) corresponding to all or part of a nucleotide fragment
Reads mapped to locus	The reads mapped to the locus for the BAM entry/file. A read refers to a sequence of base pair(s) corresponding to all or part of a nucleotide fragment
r_pb	The Pearson Correlation Coefficient value. This value is used to determine the similarity of the splice variant selected where the closer the value is to 1 shows similarity and 0 shows no similarity
RPKM	The RPKM value for the chosen RPKM mode
Controls	The BAM record/experiment number of the controls in your RNA-Seq data. Separate controls by commas

Download table as an image

You can download the table as an image file by clicking on the "Download table as an image" once you have loaded a dataset onto the eFP-Seq Browser. This will open a module which you can right click and save the display image onto your local drive.

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NOTE:

If the image looks stretched in the "Download table as an image" module, do not worry, it is just being displayed like that because of the browser. It will not look like that when downloaded.

Toggle the RNA Table

You can toggle which columns you would like to see in RNA table by clicking on the "gears"/settings icon on the bottom right of the screen once a dataset has been loaded and then clicking on the "Filter Table" tab (this is the default tab when opening the RNA-table's settings). Just check any box off that you would not like to see and that image will be toggled off (or check a box that you do want to keep displayed and it will show).

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Filter eFP Images

You can also toggle and filter which eFP images you would like to see in RNA table by clicking on the "gears"/settings icon on the bottom right of the screen once a dataset has been loaded and then clicking on the "Filter eFP Images" tab. Just check any box off that you would not like to see and that image will be toggled off (or check a box that you do want to keep displayed and it will show).

Help image for toggling and filtering eFP images from the RNA-table

To visualize your own data, there are two options to do this. If you have a BAM file but have not yet generated a readable XML file, select the "Generate Data" option. If you have already generated a readable XML file, you can directly upload these XML files by selecting the "Upload Data" option. You can enhance these options by storing your visualized data onto your private account (see more in the "Manage Person Account" help card)

Generate Data

This opens a form to fill which generates an XML which is readable by the eFP-Seq Browser to visualize your data. Any field with an asterisk at the end of it are mandatory fields to be filled for your data to be visualized properly (without it, the eFP-Seq Browser cannot visualize your data).

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The following table describes what each field requires:

Form Label	Form Input Description
Dataset Title	REQUIRED* The title of your entire dataset. This will be displayed on the navigation bar in the dataset dropdown option if you chose to store this dataset to your private account
Author(s)	REQUIRED* You and/or any other authors that contributed to the dataset
Contact info	The contact information of the authors
Title	REQUIRED* The given title for each individual BAM entry/file. It is recommended that this entry is kept short
Description	REQUIRED* A written description of each individual BAM entry/file
Record Number	REQUIRED* The SRA/SRR record number/identifier for the individual BAM entry/file
RNA-Seq Data/BAM file Repository Link	REQUIRED* A link to your individual RNA-Seq Data/BAM entry/file repository. The eFP-Seq Browser can read BAM files stored on either Google Drive or Amazon AWS. Each BAM file must be in its own folder with its BAM index file
BAM Filename	The filename of the BAM file in the repository location (with the .bam file extension)
Publication Link	A link to the published research
Sequence Reach Archive/NCBI Link	If the record number has a website describing it in more detail, that link can be posted here
Total Reads Mapped	REQUIRED* The total number of reads in the BAM entry/file. A read refers to a sequence of base pair(s) corresponding to all or part of a nucleotide fragment. If you do not know how many total reads mapped there are in your BAM file/entry, just insert 0 or leave it blank and the eFP-Seq Browser will find this value for you (NOTE: If you do input 0/blank, this will significantly increase load time).
Read map method	A description of the method that was used to map the read alignments
Species	REQUIRED* The organism that your RNA-Seq data is mapped for. Currently, the eFP-Seq Browser only supports Arabidopsis thaliana
Tissue	REQUIRED* The tissue part that your individual BAM entry/file RNA-Seq data is mapped to. If you do not know what tissue it is mapped to or your species is not Arabidopsis thaliana, it is recommended you select the "Other" option
Controls	The BAM record/experiment number of the controls in your RNA-Seq data. Separate controls by commas
Replicate Controls	The BAM record/experiment number of the replicate controls in your RNA-Seq data. Separate controls by commas

If you wish to reset the form and return it the default empty form with one entry, you can click on the "Reset Form" button to do that.

If it is easier for you to fill an Excel (XLSX) template (which you can save and continue at any time), you can download our Excel template to generate the readable XML and then click the "Upload Excel" button to fill the form out.

For the most part, the Excel template follows the same format as the form with the exception of the hidden field "Tissue subunit*" which in the Excel template, you are going to have to fill manually.

For the column "Tissue subunit*", there is a dropdown of options that correspond with the tissue that you select. Please fill it appropriately with the correct option name from the dropdown. If you do not fill this correctly, this will default to either "all" or a respective correct tissue subunit.

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NOTE:

For the Excel template, it is recommended for the following columns you do not manually type in your options but rather use the Dropdown option as it will prevent any errors from arising:

Repository type*
Species*
Tissue*
Tissue subunit*

To convert the Excel data, copy and paste your fill Excel template into the "Upload Excel" form (in Excel, Select all and then in the eFP-Seq Browser's Upload Excel, Paste), click the "Convert Data" button and let it load. If your Excel data has more than 50 datasets, it may take >5 to convert the data and the eFP-Seq Browser will be unresponsive during this time.

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NOTE:

For the Excel converter to work correctly ("Upload Excel"), you need to also insert row 1 of the of the Excel template:
"Title* Description* Record Number * RNA-Seq Data/BAM file repository link* BAM Filename* Repository type* Publication Link SRA/NCBI Link Total Reads Mapped* Read Map Method Species* Tissue* Tissue subunit* Controls Replicate Controls"

Upload Data

Once you have an XML generated for your data, you can directly upload it to the eFP-Seq Browser at any time. To do so, click on the "Upload Data" button in the navigation menu on the left side of the eFP-Seq Browser.

If you are logged into your private account, you will be prompted with the option if you want to upload the XML to your private account. If selected "YES", then this XML will be accessible at any time you are logged in without the need to upload again.

If you wish to learn more about the XML file and its attributes, you can check out the "XML Parameters" help card or if you wish to learn more about your private account and how to manage it, you can check the "Manage Personal Account" help card.

The first XML element is the "files" element which consists of the following attributes:

Attribute name	Attribute description
xmltitle	The title of the entire dataset. This will be displayed on the navigation bar in the dataset dropdown option if uploaded
author	The author(s) that contributed to or created the dataset
contact	The contact information of the authors

Following the "files" element, each individual BAM entry/file will consist of its own subelement to "files" called "file". The "file" subelement consists of the following attributes:

Attribute name	Attribute description
info	A written description of each individual BAM entry/file
record_number	The SRA/SRR record number/identifier for the individual BAM entry/file
foreground	Used in opening the visualized data in the IGB viewer. Use this field to define annotation or graph colours in the IGB viewer
hex_colour	Used to define annotation or mapping colours of the visualized RNA-Seq images
bam_type	Where the BAM repository is stored. Currently, the only options that exist are "Amazon AWS" and/or "Google Drive"
name	A link to each individual RNA-Seq Data/BAM entry/file repository. The eFP-Seq Browser can read BAM files stored on either Google Drive or Amazon AWS. Each BAM file must be in its own folder with its BAM index file
filename	The filename of the BAM entry respective to the .BAM and .BAI (BAM index) file
total_reads_mapped	The total number of reads in the BAM entry/file. A read refers to a sequence of base pair(s) corresponding to all or part of a nucleotide fragment
read_map_method	A description of the method that was used to map the read alignments
publication_link	A link to the published research
svg_subunit	The subunit/part of the tissue that the RNA-Seq mapped alignment correspond with. To find a list of all tissues subunits, please see the "Tissue Selection Options" sheet in our Excel template
svgname	The tissue part that your individual BAM entry/file RNA-Seq data is mapped to. To find a list of all tissues, please see the "Tissue Selection Options" sheet in our Excel template
species	The organism that the RNA-Seq data is mapped to. Currently, the eFP-Seq Browser only supports Arabidopsis thaliana
description	The given title for each individual BAM entry/file. It is recommended that this entry is kept short
url	If the record number has a website describing it in more detail, that link can be posted here
controls & bam_exp	The BAM record/experiment number of the controls in your RNA-Seq data. Separate by individual `<bam_exp>`
groupwith & bam_exp	The BAM record/experiment number of the replicate controls in your RNA-Seq data. Separate by individual `<bam_exp>`

The private account feature utilizes your Google account. Simply click the blue login button on the button of the navigation bar to login into your eFP-Seq Browser private account.

After logging in, whenever you upload an XML you will be prompted with the option if you want to upload the XML to your private account. If selected "YES", then this XML will be accessible at any time you are logged in without the need to upload again.

To manage your account and what XML/datasets are uploaded to your account (or to redownload them), select the "Manage Account" option in the navigation bar. In this modal, you will have the option to download existing XML/datasets or to delete private datasets from your account.

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NOTE:

If you select any of the public datasets in the "Manage account" option, the ability to delete datasets will be disabled. To delete datasets, make sure public datasets are unchecked.

Deleting your account

If you wish to delete your account, you can do so whenever you are logged into your account and then simply open the "Manage account" option and click the "Delete Account" button. This will prompt a warning and confirmation before you are able to fully delete your account.

NOTE:

If you chose to delete your account, this action is permanent and you cannot recover your account or its data once it has been deleted.

If you are curious about our privacy or cookie policy, you can click here to learn more.

We welcome feedback on the eFP-Seq Browser to nicholas.provart@utoronto.ca. You can also reach us on Twitter at @BAR_PlantBio

Also, if found any bugs, would like any features added to accommodate your needs or we would simply like to tell us how much you enjoyed using the eFP-Seq Browser, feel free to email or Tweet at us.

Cookie Policy
Privacy Policy

It is your cookies!

Do we use cookies?
Yes. As described in our Privacy Policy, we use cookies and other technology to ensure the best possible experience for you while using the eFP-Seq Browser.

What Are Cookies?
A cookie is a small file of information sent to your browser whenever you visit a website. These tiny files are used to store information about you and your preferences while you visit a site. This information is then used to give you the same or similar experience as you had before when you visit the site again.

What cookies do we use?
The following table below describes most of the cookies we intentionally use in the eFP-Seq Browser. These may include third-party cookies.

Category of Use	Description
Account related cookies	Of you create an account with us, we will use cookies to manage the signup and login/admission process. These cookies can be used to keep you logged in or keep any preferences you had from your previous visit.
Google Analytics	The eFP-Seq Browser uses Google Analytics (a trusted analytics platform) to help understand how you use our site and to help us then improve your quality and experience with our web-tool. These cookies may track things such as how long you spend using the eFP-Seq Browser. For more information on Google Analytics cookies, see the official Google Analytics page.

Disabling Cookies
Most browsers allow you to control cookies through its setting preferences. Be aware, disabling cookies may affect the functionality of the eFP-Seq Browser and many other sites that you visit. It is recommended that you do not disable your cookies. You can learn more about how to manage your cookies by either following for the hyperlink for Chrome.

More Information
We hope this clarifies information about cookies. However, if you are still looking for more information then you can contact us through one of our preferred contact methods:

Email: nicholas.provart@utoronto.ca
Twitter: @BAR_PlantBio

Your Privacy Matters!

Your privacy online and through our services is important. With the eFP-Seq Browser, we provide you with a free service which allows you to visualize and analyze your RNA seq-based genomic information. This Privacy Policy applies to the use of this service.

What we collect?
1. Upon Registration
2. Upon Using Our Service
3. Cookies
4. Data Collected from Others
How we use your data
1. Account and personal data
2. Information collected upon use of our service
Sharing information
1. Your account and personal data
2. Information we collect
3. Legal disclosure
Your Data
1. Data retained
2. Right to Access and Control

It is important to note that our privacy policy is an extension of the University of Toronto Privacy Policy and is exclusive to the Bio-Analytic Resource (BAR) and it’s eFP-Seq Browser.

Welcome to the Arabidopsis thaliana eFP-Seq Browser