StrengthTrainer GLSY22522, User Manual

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Section 8: Conversion of gene symbols to Entrez IDs
Expression data
If the expression data and interactome data contain gene labels in different formats, i.e.
one corresponds to Entrez IDs and the other to gene symbols, then the gene symbols are
mapped to Entrez IDs. For the mapping process, we utilize the Bioconductor [18]
annotation files and, in some instances, the gene symbol to Entrez ID mapping is
unavailable. The list of gene symbols that could not be mapped to Entrez IDs is saved in
the following files –
a.
Error_Expr.txt : This file contains the gene symbols that were present in the
expression data but could not be mapped to Entrez IDs.
b.
Error_PPI_Hubs.txt : This file contains the hubs for which the gene symbols could not
be mapped to Entrez IDs.
c.
Error_PPI_Int.txt : This file contains the interactors for which the gene symbols could
not be mapped to Entrez IDs
Interactome data
The functions generatePpiMap and generateMicroRnaMap are used to generate the
interactome data files. These functions return the hub-interactor pairs in two formats –
one corresponding to Entrez IDs and the other to gene symbols. As mentioned earlier, in
some instances, the Entrez ID to gene symbol mapping is unavailable and the Entrez IDs
that could not be mapped to gene symbols are saved in the following files –
a.
Error_Mirnome_Generation.txt : This file contains the microRNA-gene pairs for which
the Entrez IDs could not be mapped to gene symbols
b.
Error_PPI_Generation.txt : This file contains the gene-gene pairs (hub-interactor pairs)
for which the Entrez IDs (for at least one of the genes in the pair) could not be
mapped to gene symbols.