Biomedical Engineering Reference
In-Depth Information
$ head gene.go
ENSMUSG00000000001
$ head gene.go
ENSMUSG00000000001
membrane_fusion . . .
membrane_fusion . . .
ENSMUSG00000000028
ENSMUSG00000000028
DNA-dependent_DNA_replication . . .
DNA-dependent_DNA_replication . . .
ENSMUSG00000000049
ENSMUSG00000000049
acylglycerol_metabolism angiogenesis . . .
acylglycerol_metabolism angiogenesis . . .
ENSMUSG00000000058
ENSMUSG00000000058
M_phase_of_mitotic_cell_cycle . . .
M_phase_of_mitotic_cell_cycle . . .
ENSMUSG00000000078
ENSMUSG00000000078
cytokine_and_chemokine_mediated_sign . . .
cytokine_and_chemokine_mediated_sign . . .
ENSMUSG00000000085
ENSMUSG00000000085
gene_silencing
gene_silencing
ENSMUSG00000000093
ENSMUSG00000000093
aging cardiac_muscle_development . . .
aging cardiac_muscle_development . . .
ENSMUSG00000000094
ENSMUSG00000000094
angiogenesis appendage_development . . .
angiogenesis appendage_development . . .
ENSMUSG00000000120
ENSMUSG00000000120
axon_guidance axonogenesis cell_proj . . .
axon_guidance axonogenesis cell_proj . . .
ENSMUSG00000000125
ENSMUSG00000000125
Wnt_receptor_signaling_pathway . . .
Wnt_receptor_signaling_pathway . . .
As an input, permutation_test needs to take a fi le containing three TAB-
separated fi elds: the fi rst fi eld is an id (e.g. gene id), the second fi eld is a
value (e.g. density) and the third fi eld is a SPACE-separated list of
annotations. We fi rst group the results in 'tss.val' by gene using 'vector
-merge', then choose the maximum density per gene across transcripts
using 'vector-max', and fi nally perform a join operation with 'gene.go'
(note that the delimiter used in the join operation specifi ed by option '-t'
must be a TAB, i.e. Control-V-I):
$ cat tss.val | tr ':' '\t' | cut -f1,3 | sort | uniq | vectors -merge
-n 6 | vectors -max -n 6 | join -a1 -t ' ' - gene.go > tss.val+go
$ cat tss.val | tr ':' '\t' | cut -f1,3 | sort | uniq | vectors -merge
-n 6 | vectors -max -n 6 | join -a1 -t ' ' - gene.go > tss.val+go
$ head tss.val+go
ENSMUSG00000000544
$ head tss.val+go
ENSMUSG00000000544
0.000000
0.000000
ENSMUSG00000000817
ENSMUSG00000000817
0.000000 I-kappaB_kinase/NF-kappaB_cascade . . .
0.000000 I-kappaB_kinase/NF-kappaB_cascade . . .
ENSMUSG00000001138
ENSMUSG00000001138
0.849960
0.849960
ENSMUSG00000001143
ENSMUSG00000001143
1.549900
1.549900
ENSMUSG00000001305
ENSMUSG00000001305
0.524970
0.524970
ENSMUSG00000001674
ENSMUSG00000001674
0.399980
0.399980
￿ ￿ ￿ ￿ ￿
ENSMUSG00000002459
ENSMUSG00000002459
0.000000 negative_regulation_of_signal . . .
0.000000 negative_regulation_of_signal . . .
ENSMUSG00000002881
ENSMUSG00000002881
0.774960 Schwann_cell_differentiation . . .
0.774960 Schwann_cell_differentiation . . .
ENSMUSG00000003134
ENSMUSG00000003134
0.049998 regulation_of_GTPase_activity . . .
0.049998 regulation_of_GTPase_activity . . .
Now, we can run the permutation_test tool (for details about the tool's
options the reader is referred to the User's Manual):
$ permutation_test -v -h -S n -a -p 10000 -q 0.05 tss.val+go > peaks.
enriched.go.in.tss.txt
$ permutation_test -v -h -S n -a -p 10000 -q 0.05 tss.val+go > peaks.
enriched.go.in.tss.txt
$ head peaks.enriched.go.in.tss.txt
CATEGORY
$ head peaks.enriched.go.in.tss.txt
CATEGORY
CATEGORY-SIZE
CATEGORY-SIZE
Q-VALUE P-VALUE STATISTIC
Q-VALUE P-VALUE STATISTIC
M_phase_of_mitotic_cell_cycle
M_phase_of_mitotic_cell_cycle
13
13
0.00e+00 0.00e+00 13
0.00e+00 0.00e+00 13
regulation_of_lymphocyte_activation
regulation_of_lymphocyte_activation
12
12
6.92e 03
6.92e 03
 
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