TriPOINT
A pathway analysis tool that integrates non-coding regulators for further gene prioritization.
User Manual: https://github.uconn.edu/raw/ajt06004/TriPOINT/master/UserManual.pdf
Binary file: https://github.uconn.edu/ajt06004/TriPOINT/raw/master/tripoint.jar Note: RServe will need to be installed and started in R. See the User Manual for a guide to set this up.
Available datasets are in the data directory.
Usage: java -jar tripoint.jar expression file -db pathway database -o output directory
Parameters
-db Sets pathway database to import pathways from GRAPHITE. Values available: "kegg", "reactome", "biocarta", "humancyc", "nci", "panther"
-o Sets output directory for saving result files. REQUIRED
-gid Sets the conversion method for gene identifiers. Refer to 'convertIdentifiers' in GRAPHITE. Default: "SYMBOL" (Currently other identifiers are not recommended)
-up Sets the up-regulated gene threshold. Default: 0.05
-down Sets the down-regulated gene threshold. Default: -0.05
-w Sets the weak activation/inhibition factor. Default: 0.5
-p Controls the impact of gene expression when calculating measures. Default: 0.25
-r Controls the rate of exponential decay to control edge distance in impact score calculation. Default: 0.25
-perm Sets the number of permutations for p-value calculations. Default: 10000
-rstate Sets the random state for reproducible results. Default: Current Time (milliseconds)
-refflat Specifies the UCSC refflat file to use to identify TSS locations of genes in pathways. Required for identifying non-coding regulators. Gene identifiers will need to match those provided in the expression file.
-ci Sets the tab-delimited file for chromatin interaction data to identify non-coding targets of genes
-nct Sets the bed file for non-coding targets to be associated with genes. If chromatin interactions are provided these sites will be connected via chromatin interactions, otherwise it will be proximity based
-prox Sets the proximity based non-coding target threshold which spans the base pair distance both upstream and downstream from the transcription start site. Default: 50000