Background

The Background tool generates a connection table for a sub-network search (greedy algorithm or genetic algorithm). You can provide a flag to select specific information sources.

Usage : background [OPTION]
Options:
    -p           pattern
    -o           output file
Example:
background -p 256 -o mint
background -p 4064 -o ppi 

Input

Pattern

Type Name Pattern Count
GX PCC 1 0
GX MI 2 0
LIT NLP 4 6397
LIT NCBI 8 30789
LIT COMMENTIONED 16 0
PPI HPRD 32 3346
PPI INTACT 64 8859
PPI REACTOME 128 15943
PPI MINT 256 2106
PPI MIPS 512 0
PPI DIP 1024 127
PPI KEGG 2048 4023
TF JASPAR 4096 27
TF PANTHER 8192 1768
TF KEGG 16384 140
TF PAP 32768 0

*GX: gene expression; LIT: literature; PPI: protein-protein interaction; TF: transcription factor - gene target
*PCC: Pearson correlation coefficient; MI: mutual information; NLP: natural language procession; NCBI: NCBI curated; COMMENTIONED: gene pairs commentioned in the same PubMed abstract

Gene list file

203,
11012

Output

Output file is a tab-delimited text whose first column value is source gene and rest column values are target genes.
3303	10010	11035	5971	5886	7133	4215	23118	10454	8737	4791	7189	10392	7185	9641	8767	8717
9616	140460	142689	140459
9782	23405	27161	26523
9921	55791

Last edited Feb 8, 2013 at 5:47 AM by yongkeecho, version 4

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