Annotation Feature Analysis

Question

psalguero · Accepted Answer

The analysis of annotation features provides... Note: Will include content from the research paper, once it becomes available

Annotation Features Diversity Analysis (FDA)

The diversity of annotation features among gene isoforms... Note: Will include content from the research paper, once it becomes available

When using the application, all FDA parameters are described in the Help page which can be accessed via the Help button located on the bottom left of the dialog window.

FDA Results

The FDA results are displayed in a table on the FDA Results subtab. The subtab is contained in the project data tab located in the top tab panel, see image below. Each table row displays the diversity results for a given gene. The result columns are grouped into transcript, protein, and genomic annotations. Each column within a group displays the Varying/NotVarying results for the corresponding feature. Blank row cells indicate the feature was not present for the given gene.

FDA Results Summary

The FDA Summary data visualization subtab provides results summary information. The subtab is contained in the project data visualization tab located in the bottom tab panel, see image below. The chart on the left provides varying percentages for each annotation feature at the gene level. The chart on the right provides varying percentages for each annotation feature using pairwise gene isoforms comparisons. As expected, the varying percentages using the pairwise isoforms are lower.

Differential Feature Inclusion Analysis (DFI)

To perform Feature-level differential splicing analysis, you choose what features you will like to include. You also need to specify if you want the features among gene isoforms to be compared using presence or genomic position overlap. The former just checks for the feature being present and having the same count. The latter checks for a genomic position overlap match for each instance of the feature. Just like in regular DIU, you may choose which R package to use, DEXSeq or edgeR. Note: Will include content from the research paper, once it becomes available

When using the application, all DFI parameters are described in the Help page which can be accessed via the Help button located on the bottom left of the dialog window.

DEXSeq

DEXSeq provides "...".You may view the documentation and installation instructions at:

https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html

edgeR

EdgeR provides "...".You may view the documentation and installation instructions at:

https://www.bioconductor.org/packages/release/bioc/html/edgeR.html

DFI Results

The DFI results are displayed in a table on the DFI Results subtab. The subtab is contained in the project data tab located in the top tab panel, see image below. Each table row displays the same information as in the regular DFI, the difference being in the rows containing a specific annotation feature in addition to the gene.

DFI Results Summary

The DFI results summary table summarizes the results by feature. For each feature, it displays the number of feature DIU genes detected as well as the number of tested and total genes. Tested genes is the actual number of genes tested for DIU, that is genes having multiple isoforms and varying feature. Total genes is the number of genes containing the feature. The number of DIU genes favoring each condition is also displayed. Each table row displays the same information as in the regular DIU, the difference being in the rows containing a specific annotation feature in addition to the gene.

DFI Results Gene Association

The DFI results gene association table explores the association of two features to any given gene. For each pair of features, it displays the number of genes where both features were found to be DS. In addition, the counts for genes where the features were favored in the same or opposite conditions are shown.