; 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 ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71 ; Host name rsat-tagc ; Job started 2022-03-03.092844 ; Job done 2022-03-03.092858 ; Seconds 0.15 ; user 0.15 ; system 0.03 ; cuser 10.82 ; csystem 0.71