; network-interactions  -v 20 -title demo_01 -tfs $RSAT/public_html/demo_files/TFs_short.txt -cre $RSAT/public_html/demo_files/enhancers_short.bed -genome galGal4 -report_net -net $RSAT/public_html/demo_files/net_short.tsv -score 5 -pval 0.0005 -outdir ./Demo_01 -html
; Input files
;	TFs          	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/TFs_short.txt
;	network      	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/net_short.tsv
;	cres         	/home/rsat/packages/rsat-2021/rsat/public_html/demo_files/enhancers_short.bed
; Results files
;	network_intersection_onlyTFs	./Demo_01/ResultsFiles/network_intersection_onlyTFs_2022-03-03.092844.tsv
;	GRN_indirect_interactions	./Demo_01/ResultsFiles/GRN_indirect_interactions_2022-03-03.092844.tsv
;	archive      	./Demo_01/network-interactions_archive_2022-03-03.092844.zip
;	network_not_found_interactions	./Demo_01/ResultsFiles/network_not_found_interactions_2022-03-03.092844.tsv
;	err_log      	./Demo_01/ResultsFiles/_errors.txt
;	log          	./Demo_01/ResultsFiles/network-interactions_log_2022-03-03.092844.txt
;	network_intersection	./Demo_01/ResultsFiles/network_intersection_2022-03-03.092844.tsv
;	network_found_interactions	./Demo_01/ResultsFiles/network_found_interactions_2022-03-03.092844.tsv
;	summary      	./Demo_01/ResultsFiles/SUMMARY_2022-03-03.092844.html
;	GRN_direct_interactions	./Demo_01/ResultsFiles/GRN_direct_interactions_2022-03-03.092844.tsv
;	complete_direct_interactions	./Demo_01/ResultsFiles/complete_direct_interactions_2022-03-03.092844.tsv
; Intermediate files
;	used_regulatory_regions	./Demo_01/IntermediateFiles/network-interactions_used_regulatory_regions_2022-03-03.092844.bed
;	used_cre_seqs_geneheader	./Demo_01/IntermediateFiles/network-interactions_used_cre_seqs_geneheader_2022-03-03.092844.fa
;	used_matrixes	./Demo_01/IntermediateFiles/network-interactions_used_matrixes_2022-03-03.092844.tf
;	used_matrix_scan_results	./Demo_01/IntermediateFiles/network-interactions_used_matrix-scan_results_2022-03-03.092844.tsv
;	used_cre_seqs	./Demo_01/IntermediateFiles/network-interactions_used_cre_seqs_2022-03-03.092844.fa
# Report of 3-nodes direct interactions
# cases of no direct interactions are specified.
#node1 ==> node2 ==> node3


LMX1B	==>	IRX1
LMX1B	IRX1	chr2:87130510-87131509	D_149_159;D_8_18	1.2;2.0


LMX1B	==>	TFEB	==>	IRX1
LMX1B	TFEB	chr26:4959032-4960031	R_315_325;D_844_854;R_641_651;R_172_182;D_312_322;R_847_857	6.7;8.6;0.7;1.6;7.5;7.3
==>
TFEB	IRX1	chr2:87130510-87131509	D_163_172	5.7


LMX1B	==>	TFEB	==>	YY1
LMX1B	TFEB	chr26:4959032-4960031	R_315_325;D_844_854;R_641_651;R_172_182;D_312_322;R_847_857	6.7;8.6;0.7;1.6;7.5;7.3
==>
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8


LMX1B	==>	YY1	==>	LMX1B
LMX1B	YY1	chr5:48408565-48409521	R_302_312;D_299_309	1.9;2.0
==>
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2


LMX1B	==>	YY1	==>	EYA1
LMX1B	YY1	chr5:48408565-48409521	R_302_312;D_299_309	1.9;2.0
==>
YY1	EYA1	chr2:116791463-116792812	R_370_381	5.1
YY1	EYA1	chr2:116685751-116686124	D_199_210	4.2


LMX1B	==>	YY1	==>	TFEB
LMX1B	YY1	chr5:48408565-48409521	R_302_312;D_299_309	1.9;2.0
==>
YY1	TFEB	chr26:4959032-4960031	R_292_303	7.8


LMX1B	==>	YY1	==>	SOX11
LMX1B	YY1	chr5:48408565-48409521	R_302_312;D_299_309	1.9;2.0
==>
YY1	SOX11	chr3:93974046-93974675	D_47_58	4.5

IRX1 has no targets.

TFEB	==>	IRX1
TFEB	IRX1	chr2:87130510-87131509	D_163_172	5.7


TFEB	==>	TFEB
TFEB	TFEB	chr26:4959032-4960031	R_821_830;D_821_830	5.8;6.7


TFEB	==>	YY1	==>	LMX1B
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8
==>
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2


TFEB	==>	YY1	==>	EYA1
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8
==>
YY1	EYA1	chr2:116791463-116792812	R_370_381	5.1
YY1	EYA1	chr2:116685751-116686124	D_199_210	4.2


TFEB	==>	YY1	==>	TFEB
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8
==>
YY1	TFEB	chr26:4959032-4960031	R_292_303	7.8


TFEB	==>	YY1	==>	SOX11
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8
==>
YY1	SOX11	chr3:93974046-93974675	D_47_58	4.5


YY1	==>	LMX1B	==>	IRX1
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2
==>
LMX1B	IRX1	chr2:87130510-87131509	D_149_159;D_8_18	1.2;2.0


YY1	==>	LMX1B	==>	EYA1
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2
==>
LMX1B	EYA1	chr2:116791463-116792812	D_419_429;R_422_432;D_416_426	1.2;9.0;1.4


YY1	==>	LMX1B	==>	TFEB
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2
==>
LMX1B	TFEB	chr26:4959032-4960031	R_315_325;D_844_854;R_641_651;R_172_182;D_312_322;R_847_857	6.7;8.6;0.7;1.6;7.5;7.3


YY1	==>	LMX1B	==>	YY1
YY1	LMX1B	chr17:10117169-10118087	R_271_282	5.2
==>
LMX1B	YY1	chr5:48408565-48409521	R_302_312;D_299_309	1.9;2.0


YY1	==>	TFEB	==>	IRX1
YY1	TFEB	chr26:4959032-4960031	R_292_303	7.8
==>
TFEB	IRX1	chr2:87130510-87131509	D_163_172	5.7


YY1	==>	TFEB	==>	YY1
YY1	TFEB	chr26:4959032-4960031	R_292_303	7.8
==>
TFEB	YY1	chr5:48408565-48409521	D_210_219;R_8_17;R_210_219	6.2;5.7;9.8

; Host name	rsat-tagc
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; Job done	2022-03-03.092858
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