GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine

BMC Genomics

Table 1 Comparison between GMIEC and others bioinformatic tools available in precision medicine

Name resource	Type application	Uploading custom data	Input file	GUI interface	Reference
GMIEC	Web-based/ shiny application	yes	Gene-expression, copy number, methylation, table with genes mutated, drugs-genes file, clinical data, gene-list, bed file.	yes	–
DriverDBv3	Web-based	no	The web interface incorporates somatic mutations, RNA-seq, miRNA-expression, methylation, copy number, clinical data.	yes	[12]
OncoKB	Web-based	no	Users can query the database gene, alteration, drug	yes	[13]
PanDrugs	Web-based	yes	VCF, RNK, gene-lists, drug query	yes	[8]
PreMedKB	Web-based	no	Users can query the resource for variant, disease, drug, gene or combinations of these category.	yes	[6]
Cancer Variant Explorer	R-package	yes	Clinical, mutation	no	[14]
IndividPath	R-package	yes	Gene-expression	no	[15]
iPAS	R-package	yes	Gene-expression	no	[16]
PharmacoGx	R-package	no	Pharmacogenomic datasets	no	[17]
Prodigy	R-package	yes	Protein-protein interaction network, gene-expression, mutations	no	[18]

Table 1. Comparison the bioinformatics tools and databases that can be used in the context of precision medicine. The column “name resource” contains the name of the software/database. The second column (“Type application”) described if a tool is a R-package or a web-based application. For each tool, the input file required for the analysis are reported in column (“Input file”). The column “GUI interface” highlight if a given tool/database was implemented with a GUI interface or not.

ISSN: 1471-2164