Overview

The GeneList tool allows the user to search for genes using gene IDs, descriptions, experiments, GO ids and different annotations, and then saves the result in a list that can be used by other tools.

Basic Usage Simply type in gene ids, descriptions, or different annotations. The matching genes will be displayed with selected annotations. The result can be customized by clicking the Select Displayed Annotations button. There are three buttons to “Save all to Gene List”, “Remove selected from Gene List” or “Empty Gene List”. The “Share table” button allows sharing the current GeneList with other users by way of an auto generated URL. The GeneList tool is the starting point for most PlantGenIE workflow.

Multiple GeneList The GeneList tool is capable of holding several named gene lists for use in other tools. These lists can be Added, Renamed or Deleted. Once clicking on a GeneList name, it will become the active GeneList and will be displayed in all other tools. GeneLists will remain for seven days while shared GeneList will be saved for 30 days.

Data

We use both PostgresSQL and MySQL to store annotation data. The GeneLists tool uses both in house annotation data and data from Phytozome and Plaza.

Implementation

This tool uses JavaScript, PHP, MySQL, PostgreSQL, JQuery, Datatables and Toastr libraries. SQL views and tmp tables gave additional speed to the tool.

Overview

The BLAST (Basic Local Alignment Search Tool) tool compares input sequences to PlantGenIE sequence databases to identify homologous sequence matches.

Basic Usage

Simply paste your sequence (with or without a FASTA header) into the Query Sequence input text box. Alternative you can retrieve a transcript sequence by entering a gene ID into the Load example text box, or you can upload a sequence file (Less than 100 MB) using the upload file function. Having used one of these input options, click and select the desired dataset from the lists of available BLAST databases. Finally click the BLAST! button at the bottom of the page.

PlantGenIE BLAST uses standard default NCBI BLAST options. However users can change the following advanced options:

Option Description
Scoring matrix Substitution matrix that determines the cost of each possible residue mismatch between query and target sequence. See BLAST substitution matrices for more information.
Filtering Whether to remove low complexity regions from the query sequence.
E-value cutoff The maximum expectation value of retained alignments.
Query genetic code Genetic code to be used in blastx translation of the query.
DB genetic code Genetic code to be used in blastx translation of the datasets.
Frame shift penalty Out-of-frame gapping (blastx, tblastn only) [Integer] default = 0.
Number of results The maximum number of results to return.

BLAST results

The BLAST Results page will be automatically reloaded until the search results are successfully retrieved. BLAST results are organized into a table containing Query ID, Hit ID, Average bit score (top), Average e-value (lowest), Average identity (av. similarity) and Links. Clickable BLAST results display the corresponding region of identified homology within the GBrowse tool, where the matching region is shown.

Data

The BLAST tool uses public genome assemblies, early release de novo assemblies from UPSC and data from [Phytozome] (http://www.phytozome.net/) and Plaza.

Implementation

PlantGenIE BLAST search is implemented using NCBI Blast (v2.2.26) and a backend PostgresSQL Chado database. We use PHP, JavaScript, XSL, Perl and d3js, Drupal libraries to improve Open Source GMOD Bioinformatic Software Bench server to provide a graphical user interface.


Overview
GBrowse is an open-source, genome annotation viewer.

Basic Usage
To find particular region of the chromosome, type a gene name, a short sequence (minimum of 15 bp), or a nucleotide range in the Landmark or Region box located near the top left of the page and click on the Search button. The area shown in the Details panel is highlighted by a box. You can grab the box and slide it left or right within limits (it can't slide over the whole genome). Once you get to a particular location, you can fine-tune the view with the Scroll/Zoom buttons to move along the chromosome or change magnification.

Data
GBrowse uses in house annotation data and data from Phytozome and Plaza.

Implementation
PlantGenIE GBrowse uses customized version of Generic Genome Browser version 2.49. We use dedicated GBrowse servers for each of our PlantGenIE resources.


Overview
exImage provides an intuitive pictographic view of expression data across a diverge range of PlantGenIE datasets.

Basic Usage
Users can either enter a gene ID in the input text area (and hit the "GO" button) or create a gene list which then will appear as an interactive list in the tool. exImage will shade the samples according to expression levels across multiple samples using either absolute or relative values. Relative values displays expression relative to the mean expression across all samples. The current view can be exported in various vector formats including publication ready PDFs or as expression values. The ‘Take a tour’ feature will provide a brief introduction to the basic functionalities in exImage.

Data
exImage uses VST (Variance-Stabilizing Transformation) values for absolute expression, and no unit for the relative values. Absolute expression values were generated by aligning RNA-Seq reads to the reference genome and gene annotation with aligned read numbers then used to calculate VST values.

Implementation
exImage was developed using PHP, Javascript, d3js, rsvg-convert, imagemacgick, librvg and batik. exImage uses a MySQL database as a backend data source. exImage was inspired by the eFP resource.

Overview
exPlot is an interactive plotting tool visualize expression profiles as line graphs for selected genes and experiments.

Basic Usage
Type in multiple gene IDs in the input text area separated by comma, space, tab or new line and hit the "Search" button. Alternatively, you can create a gene list, in which case genes from the currently active list will be displayed. The tool plots VST normalized gene expression values across the selected samples or pre-defined sets of samples for the input genes. Different sample sets are available in the ‘SampleList’ in the top-right corner of the page. The plot is interactive and allows the user to select a subset of the displayed genes and to create a new GeneList containing only these genes. Publication-ready figures, in PDF or SVG format, can be exported

The ‘Take a tour’ feature will provide a brief introduction to the basic functionalities available in exPlot.

Data
exPlot uses the same VST(variance-stabilizing transformation) datasets stored in MySQL database.

Implementation
exPlot was developed using JavaScript, PHP and MySQL. It uses Highchart open source framework to visualize, draw and export charts interactively.

Overview
The Chromosome diagram tool plots the location of genes in the active gene list.

Basic Usage
Type in multiple gene ids inside the input text area separated by comma, space, tab or new line and hit the "Submit" button. Click the padlock icon to enable zoom in function. You can scroll or use the zoom slider to zoom in or zoom out the chromosome diagram. When you mouse over the gene location, it will show the detailed information popup and link to the Gene Information page. You can simply drag and select the favorite gene locations and export as TSV or GFF3; or visualize in Phytozome or Agrigo. The Chromosome diagram tool allows users to upload a gene list and display the chromosomal location of those genes. It has controllers to change the color of the output diagram and also generates publication-ready plot that can be exported in common file formats including PDF.

Data
The Chromosome diagram tool uses basic annotation data from PlantGenIE MySQL database and you can upload custom files.

Implementation
The Chromosome diagram tool was built using Action script, PHP and MySQL.

eXHeatmap
This tool is generates a heatmap plot, useful for clustering and for analyzing the expression of genes relative to each other. The network analysis tool (Popnet) is a useful alternative to clustering, while the expression plotting tool (exPlot) can be a useful alternative for plotting expression profiles. This tool uses the current gene list and sample list available in the Master Menu, so if those lists are empty, users must first fill them up from a set of dedicated tools.

Clustering with the heatmap
The genes are clustered based on the choice of a distance function and the result of the clustering is shown by means of a dendogram, that can be places on either of x and y axes. The color scale indicates how far the actual expression values are from the local consensus. Distance functions are quantifying how similar is the expression of two genes/samples. For more accurate estimators of gene expression similarity use the PopNet tool. Based on the all-pair distance estimations the genes are clustered together using a chosen variety of the hierarchical clustering algorithm. The sample information is selectable from the command panel. By clicking on the heatmap itself you will open a publishing-ready pdf, or you can export the heatmap data from the command panel and import it into your favorite plotting program.

Best tips to try before you contact us!
We have found that many apparent problems with tools in PlantGenIE can result from previous results that have been cached. Before reporting a bug/problem we would request that you first clear your browser cache, quit the browser, again clear the cache when you re-open the browser and then finally check that the problems remains.



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