Table 1:
Summary of features that are freely available at the PseudoFuN website
| PseudoFuN feature | Additional description |
|---|---|
| Interactive visualization of PGG family networks including the query pseudogene/gene | Users can query any single gene or pseudogene symbol, e.g., PTENP1. Nodes are colored by sub-clusters within the network. |
| Functional enrichment analysis of PGG family | Functional enrichment can be conducted on the genes within the PGG family on Biological Process, Molecular Function, or Cellular Components annotations. The GO functional enrichment is calculated with (i) Fisher exact test [55], (ii) Kolmogorov-Smirnov Classic [56], or (iii) Kolmogorov-Smirnov Elim [56]. |
| Genomic loci mapping of PGG family | The genes in the PGG family can be mapped back to the genome using a circus plot to identify potential loci of interest. |
| Data download for all of the figures | Users can also download results including (i) the DPgE table for all pseudogenes in the selected cancer, (ii) the gene and pseudogene expression, (iii) miRNA correlation table. |
| Links to other gene databases for more information | By directly clicking the node in the network, users can open the GeneCards and Ensembl websites [43, 57] for detailed gene information. |
| Gene/pseudogene co-expression analysis across the entire TCGA | Once a PGG family has been identified the gene/pseudogene co-expression matrix is calculated across 1 of the 32 available TCGA cancer types. |
| Tumor vs normal DE of genes/pseudogenes across all TCGA cancer types | The gene/pseudogene DE is calculated for all members of the selected PGG family. There is also an option to run DE on a specified cancer for all pseudogenes, which can be viewed or downloaded as a table. |
| Predicted miRNA targets involved in the PGG families across all TCGA cancer types | The miRNA targets involved in the selected cancer and PGG family are displayed to show which miRNAs could regulate the PGG family members using the miRNA correlation tables from TCGA. |
| DPgE analysis | Differential pseudogene expression is calculated for each of the pseudogenes in TCGA cancers using dreamBase expression information [20]. The online tool allows for manipulation and download of the table. |
DE: differential expression; DPgE: differential pseudogene expression.