How to interpret the results?

[a00101]

in tutorial data,

seqnames | start | end | strand | width | gene_name | hid | p | fdr | count | effectsize | count.pred | count.density | count.pred.density | eligible | p.neg | fdr.neg
17 | 7565097 | 7590856 |   | 25760 | TP53 | 14970 | 1.1e-29 | 0.00000 | 99 | 5.58 | 2.070 | 0.0878 | 0.00184 | 1127 | 1 | 1
2 | 79384132 | 79386879 |   | 2748 | REG3A | 2447 | 9e-08 | 0.00079 | 16 | 4.05 | 0.964 | 0.0305 | 0.00184 | 525 | 1 | 1
19 | 10596796 | 10614417 |   | 17622 | KEAP1 | 16561 | 1.2e-07 | 0.00079 | 30 | 3.60 | 2.480 | 0.0222 | 0.00184 | 1350 | 1 | 1
8 | 88882973 | 88886296 |   | 3324 | DCAF4L2 | 8280 | 4.3e-06 | 0.01800 | 21 | 3.27 | 2.180 | 0.0177 | 0.00184 | 1185 | 1 | 1

Interpretation of this result is that most likely a driver mutation is in the TP53 gene region. Should I interpret it like this? One step over, are TP53, REG3A, KEAP1, and DCAF4L2 statistically significant mutations developing lung adenocarcinoma?
But when you look at other programs, the resolution is very precise, not on a genetic basis, but on a single loci.

I'm not sure if FISHHOOK is a gene prioritization program or finding driver mutation program.

Please fill me in.
Thanks.

[mskilab]

fishHook prioritizes / nominates genes that harbor more mutations than you expect under the background model, does not prioritize individual mutations. If you want to look at more fine grained loci, just change the hypothesis interval set e.g. instead of genes use exons, protein domains, or single residues.

…

On Thu, Dec 12, 2019 at 2:01 AM a00101 ***@***.***> wrote: in tutorial data, seqnames | start | end | strand | width | gene_name | hid | p | fdr | count | effectsize | count.pred | count.density | count.pred.density | eligible | p.neg | fdr.neg 17 | 7565097 | 7590856 | | 25760 | TP53 | 14970 | 1.1e-29 | 0.00000 | 99 | 5.58 | 2.070 | 0.0878 | 0.00184 | 1127 | 1 | 1 2 | 79384132 | 79386879 | | 2748 | REG3A | 2447 | 9e-08 | 0.00079 | 16 | 4.05 | 0.964 | 0.0305 | 0.00184 | 525 | 1 | 1 19 | 10596796 | 10614417 | | 17622 | KEAP1 | 16561 | 1.2e-07 | 0.00079 | 30 | 3.60 | 2.480 | 0.0222 | 0.00184 | 1350 | 1 | 1 8 | 88882973 | 88886296 | | 3324 | DCAF4L2 | 8280 | 4.3e-06 | 0.01800 | 21 | 3.27 | 2.180 | 0.0177 | 0.00184 | 1185 | 1 | 1 Interpretation of this result is that most likely a driver mutation is in the TP53 gene region. Should I interpret it like this? One step over, are TP53, REG3A, KEAP1, and DCAF4L2 statistically significant mutations developing lung adenocarcinoma? But when you look at other programs, the resolution is very precise, not on a genetic basis, but on a single loci. I'm not sure if FISHHOOK is a gene prioritization program or finding driver mutation program. Please fill me in. Thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC73JEPRDGM7OZQI72F4CATQYHOUPANCNFSM4JZZ5PTQ> .