Error message

Deprecated function: implode(): Passing glue string after array is deprecated. Swap the parameters in drupal_get_feeds() (line 394 of /var/www/html/includes/common.inc).

Help

This section discribes how to make use of the functionalities of WheatGene database. Click on the tabs below to find information about each item as well as links to navigate throught this user manual.

The Home page of WheatGene is composed by four sections: the header, the feature cards, the species cards and the footer. 

Home page of WheatGene

(A)The Header

The header is composed of the logo of the database followed by a search box where user can perform searches by key words among all the content published in this web site. The result of the search can return species, genes, transcripts, tools, news, etc. 

(B)The Feature Cards

In this section, the user can find a set of cards representing the main features or tools of WheatGene. Both the name and the image on the card are quick links to its corresponding page.

(C)The Species Cards

Species cards account for each one of the organisms whose genome assemblies are allocated in the database. On each card there is one representative picture, followed by the ploidy characterization, scientific name, brief description and statistics overview with the number of genes, transcripts and predicted synteny blocks. The species name is a quick link to the species description page, whereas the links on the statistics of genes and transcripts redirect the user to the search functionality. Finally, the part of the statistics of synteny blocks has a link to the synteny viewer tool.

(D)The Footer

The footer shows the names of the sponsors of WheatGene as well as links to their web sites. Here we can find also information about the browser compatibility of WheatGene and the copyright.

The Organism Page is divided in two main parts. The left part (A) is a menu with some options to be displayed in the right side. (B) is the area where the information associated with the species is displayed.

Organism Page WheatGene

The following are the options that can be found in the menu of the left side (A).

Summary

Displays general information of the organism such as species name, common name, description and its photo.

Additional Details

Additional Details Organism Page WheatGene

Contains further taxonomic information including lineage, division and genetic code.

Cross Reference

Cross Reference Organism Page WheatGene

Provides a link to the organism page in the NCBI database.

Annotations

This option provides a summary of the GO annotated terms generated by means of the InterProScan annotation analysis.

Organism Page Wheat Gene

After selecting one GO report to view from the list, the system displays the report of GO annotated terms arranged by categories such as Biological Process, Cellular Component and Molecular function.

Each category is an expandable tree with sub-categories according to the function of the annotated terms.

All the different sub-categories are graphically represented by means of pie charts where each wedge accounts for a sub-category.

Term Information Organism Page Wheat Gene

When click on a particular term of the tree, a pop up is displayed with the relevant information of the annotated term. This information includes GO accession, ontology category, definition and synonyms

Gene Expression Histogram

It is a link to the Gene Expression Histogram tool of WheatGene.

Gene Expression Heatmap

It is a link to the Gene Expression Heatmap tool of WheatGene.

JBrowse

It is a link to the JBrowse of WheatGene to visualize the genome assembly of the selected organism.

Synteny Analysis

It is a link to the Synteny Viewer where user can visualize the predicted synteny blocks among different genomes.

The Search function allows to retrieve the list of genes and/or transcripts by means of a customizable search form.

Search Form WheatGene

Search Filters

(A) Choose one of the species of the list.

(B) Click on the type of feature that you want to search for: genes or transcripts.

(C) The source is the genome assembly where the genes or transcripts will be retrieved from. One organism can be associated to more than one genome assembly.

(D) You can indicate the location of the genes or transcripts that you want to search by choosing either a chromosome or the coordinates in the chromosome.

(E) The result set can be delimited by setting a filter on the names. You can filter on names that contain a word, match exactly a word or either start or end with a specific word.

(F) You can specify a list of genes or transcripts to search for by uploading a file with each name separated by a new line.

(G) When the parameters have been set you can press the button "Search" or reset the form by means of the button "Reset".

Search Results

Search Results WheatGene

(A) Result Table

The results of the search performed are displayed in a data table with six columns as following:

#: The number of the row.

Name: The name of the gene or transcript.

Type: The type of the retrieved data (gene or transcript).

Organism: The name of the species.

Source: Genome assembly where the feature was found.

Location: Chromosome and coordinates in the chromosome of the feature.

(B) Pagination

The results in the data table are paginated, so the table will show up to 20 rows per page. The page can be changed by choosing the desired page number in the drop down menu or by doing click on the "Next" link.

(C) Download Results

The results of the search can be downloaded as FASTA or tab-delimited format through out doing click on the respective links.

Gene expression profiles can be visualized from three different features:

Gene Expression on Gene Page

Gene Expression on the Gene Page

The histogram of the gene expression shows the expression values of a single gene on the gene description page.

Gene Expression Heatmap

Gene Expression Heatmap

A heatmap that shows the overall gene expression profiles in all of the RNA-Seq studies of a set of genes.

Gene Expression Histogram

Gene Expression Histogram

A histogram that shows the gene expression profiles of a set of genes for a particular RNA-Seq study.

Blast

BLAST

Four NCBI Blast programs are availble: blastn, blastx, blastp, tblastn.

Synteny Viewer

Synteny Viewer

This tool allows to visualize the synteny blocks of homologous genes among different genomes.

JBrowse

JBrowse

The genome browser JBrowse allows to visualize different features of each genome assembly.