Gene Expression Tutorial

GxSeq has several interfaces for quantitative expression analysis. These tools enable exploration of gene expression changes on a gene by gene basis. Users generally begin exploration with the Expression Viewer and a matrix of gene expression data. This tool also has links to details for each gene including visual representation of read density along the gene, plots of sample expression profiles, and a dynamic gene correlation table with real time results for user selected samples sets.

Expression Viewer

The expression viewer combines gene annotations with sample expression data in a tabular view. It supports filtering by user criteria and sorting by abundance on any combination of datasets. Gene annotations include functional data stored on the genome as well as custom annotations provided by users and generated from BLAST sequence alignments.

Quick links to the Expression Viewer are on the user dashboard Dashboard.
The expression viewer is also listed under the [Tools] tab.

Matrix

The Matrix builder is used to generate a table of gene expression values for a selection of samples. Each row in the table is a gene, with columns of gene annotations. A column will be added for each selected sample with the expression value of the gene in that sample. This matrix of expression data inlcudes links to view details of BLAST results, more details on the gene annotation including sequence, graphs of the expression data and a link to the genomic context.

Matrix select To generate a matrix:

Navigate to the expression viewer tool (Tools -> Expression Viewer)
Select the assembly you are interested in
Select Matrix from the 'Generate' dropdown
Check the samples you are interested in
Submit

Ratio

The Ratio builder is used to generate a table of gene expression ratios for two sample sets. Each row in the table is a gene, with columns of gene annotations. A column is added for each sample set with the average expression value of the set members. A third column displays the Ratio of Set A / Set B. This tool allows quick differential expression testing, but the fold changes generated by this tool are naive and do not take into account dispersion of gene expression or have any associated statistical test. This ratio table also includes links to view details of BLAST results and more details on the gene annotation including sequence, graphs of the expression data and a link to the genomic context.

Ratio select To generate a ratio:

Navigate to the expression viewer tool (Tools -> Expression Viewer)
Select the assembly you are interested in
Select Ratio from the 'Generate' dropdown
Check the samples you want to include in Set A
Check the samples you want to include in Set B
Submit

Co-expression Analysis

Real time coexpression analysis can be performed on a gene by gene basis. To access the coexpression tool from a gene's graph or details page select the 'Co-Expression' link on the top right.

This tool displays expression profiles of the top 1000 similar genes based on Pearson correlation coefficient. The correlation is generated in real time from a chosen sample set. Annotations, R, R², and average expression of each gene are rendered in an interactive table. Clicking a gene in the table generates a new correlation result for that gene allowing exploration of gene correlation networks.