Passenger versus Driver
Hi,
how do you interprete the oncofuse output based on the definitions below?
low P_VAL_CORR => likely passenger?
high DRIVER_PROB => likely driver?
EXPRESSION_GAIN => how are 5'/3' expressions computed?
I have these two lines for instance which seem contradictory:
1130 0 KDR Yes Exon 6 1 1138 2 2 5.616331914947E-5 0.9999999839119682 0.7550226777191273 Pleckstrin homology-like domain[Domain];Arf GTPase activating protein[Family];Pleckstrin homology domain[Domain];Arfaptin homology (AH) domain/BAR domain[Domain];Src homology-3 domain[Domain];Ankyrin repeat-containing domain[Domain];Ankyrin repeat[Repeat] Immunoglobulin-like domain[Domain];Immunoglobulin subtype 2[Domain];Immunoglobulin subtype[Domain];Serine-threonine/tyrosine-protein kinase catalytic domain[Domain];Immunoglobulin-like fold[Domain];Protein kinase, ATP binding site[Binding_site];Tyrosine-protein kinase, receptor class III, conserved site[Conserved_site];Immunoglobulin I-set[Domain];Tyrosine-protein kinase, active site[Active_site];Protein kinase-like domain[Domain];Immunoglobulin V-set domain[Domain];Tyrosine-protein kinase, catalytic domain[Domain];Protein kinase domain[Domain];Vascular endothelial growth factor receptor 2 (VEGFR2)[Family] GRB2;SRC KDR;NCK1;PLCG1;PTPN6;SHC1;SRC;VEGFA;VEGFC;NRP1;SH2D2A;SHC2;FLT4;FYN;GRB2;GRB10 0.031693123551895894 0.060912399971582896 0.0011108580362268734 0.08982267991811016 0.03377877733466933 0.01758896057545965
679 0 CLTC Yes Exon 10 31 1159 0 0 4.159324576929766E-4 0.9999996425673524 -0.33165129627027434 Zinc finger, C2H2-like[Domain] Clathrin, heavy chain/VPS, 7-fold repeat[Repeat];Clathrin, heavy chain[Family];Tetratricopeptide-like helical[Domain];Armadillo-type fold[Domain] Zinc finger, C2H2-like[Domain] CLTC;CLTA;CLTB 0.00561979753630853 0.0 3.7249030480169165E-5 0.0 0.0011034671362001604 0.018050986438399443
P_VAL_CORR
The Bayesian probability of fusion being a passenger (class 0), given as Bonferroni-corrected P-value.
DRIVER_PROB
The Bayesian probability of fusion being a driver (class 1).
EXPRESSION_GAIN
Expression gain of fusion calculated as:
[(expression of 5' gene)/(expression of 3' gene)]-1
Thanks,
Hi,
how do you interprete the oncofuse output based on the definitions below?
low P_VAL_CORR => likely passenger?
high DRIVER_PROB => likely driver?
EXPRESSION_GAIN => how are 5'/3' expressions computed?
I have these two lines for instance which seem contradictory:
1130 0 KDR Yes Exon 6 1 1138 2 2 5.616331914947E-5 0.9999999839119682 0.7550226777191273 Pleckstrin homology-like domain[Domain];Arf GTPase activating protein[Family];Pleckstrin homology domain[Domain];Arfaptin homology (AH) domain/BAR domain[Domain];Src homology-3 domain[Domain];Ankyrin repeat-containing domain[Domain];Ankyrin repeat[Repeat] Immunoglobulin-like domain[Domain];Immunoglobulin subtype 2[Domain];Immunoglobulin subtype[Domain];Serine-threonine/tyrosine-protein kinase catalytic domain[Domain];Immunoglobulin-like fold[Domain];Protein kinase, ATP binding site[Binding_site];Tyrosine-protein kinase, receptor class III, conserved site[Conserved_site];Immunoglobulin I-set[Domain];Tyrosine-protein kinase, active site[Active_site];Protein kinase-like domain[Domain];Immunoglobulin V-set domain[Domain];Tyrosine-protein kinase, catalytic domain[Domain];Protein kinase domain[Domain];Vascular endothelial growth factor receptor 2 (VEGFR2)[Family] GRB2;SRC KDR;NCK1;PLCG1;PTPN6;SHC1;SRC;VEGFA;VEGFC;NRP1;SH2D2A;SHC2;FLT4;FYN;GRB2;GRB10 0.031693123551895894 0.060912399971582896 0.0011108580362268734 0.08982267991811016 0.03377877733466933 0.01758896057545965
679 0 CLTC Yes Exon 10 31 1159 0 0 4.159324576929766E-4 0.9999996425673524 -0.33165129627027434 Zinc finger, C2H2-like[Domain] Clathrin, heavy chain/VPS, 7-fold repeat[Repeat];Clathrin, heavy chain[Family];Tetratricopeptide-like helical[Domain];Armadillo-type fold[Domain] Zinc finger, C2H2-like[Domain] CLTC;CLTA;CLTB 0.00561979753630853 0.0 3.7249030480169165E-5 0.0 0.0011034671362001604 0.018050986438399443
P_VAL_CORR
The Bayesian probability of fusion being a passenger (class 0), given as Bonferroni-corrected P-value.
DRIVER_PROB
The Bayesian probability of fusion being a driver (class 1).
EXPRESSION_GAIN
Expression gain of fusion calculated as:
[(expression of 5' gene)/(expression of 3' gene)]-1
Thanks,
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