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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.

Expression matrix 23c92f223a6f8c6fb5772b29cf621b304d3c5bf17e9ca270a6c7cdb1ff169c4f

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 a5a94c8163f2c0594283ae3a33fd855f93b34978ae030e4d0c448e480e3ed142 To generate a matrix:

  1. Navigate to the expression viewer tool (Tools -> Expression Viewer)
  2. Select the assembly you are interested in
  3. Select Matrix from the 'Generate' dropdown
  4. Check the samples you are interested in
  5. 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 f3ae9b931ed260a8525ff5345c73a5687fc71661ffb27278d3000e05d3d3c638 To generate a ratio:

  1. Navigate to the expression viewer tool (Tools -> Expression Viewer)
  2. Select the assembly you are interested in
  3. Select Ratio from the 'Generate' dropdown
  4. Check the samples you want to include in Set A
  5. Check the samples you want to include in Set B
  6. 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.

Co expression link ac02b31a91e1c80a5be64b894dd1599d951f2dbde49387f73dbb1a4c5dfdcb74


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.

Co expression graph 50e72ceb913b4907f8456ecfcf6756a25d482a802581a0b7cc77ef81018f3c91