get_promoter_region_biomartfile00 genomic information for the gene file. 2012-04-11 10:53:17.58 UTC epigen_file00 File with epigenetic information 2012-04-11 10:53:47.559 UTC epigen_file_end00 column for the end coordinate for each row in the epigenetic file info 2012-04-11 10:56:17.916 UTC epigen_file_start00 column for the start coordinate for each row in the epigenetic file info 2012-04-11 10:55:51.716 UTC epigen_file_chr00 chromosome column at the epigenetic file 2012-04-11 10:55:29.948 UTC gene_chr00 4 2013-10-04 15:26:59.847 UTC column for the gene chromosome coordinate 2012-04-11 10:57:05.49 UTC upstream00 number of base pairs for computing a promoter region upstream the transcriptional start site (TSS) 2013-10-04 15:26:21.550 UTC 5000 2013-10-04 15:26:25.295 UTC downstream00 2000 2013-10-04 15:26:09.728 UTC number of base pairs for computing a promoter region downstream the transcriptional start site (TSS) 2013-10-04 15:25:59.440 UTC overlap00 overlap parameter (in base pairs) for computing overlapping regions 2013-10-04 15:25:02.464 UTC 100 2013-10-04 15:24:51.297 UTC gene_expr_file00 file with the gene expression values 2013-10-04 15:24:33.728 UTC genes_overlap The file with the genes that overlap with the epigenetic file 2013-10-04 15:29:02.887 UTC genes_non_overlap The file with the genes that do not overlap with the epigenetic file 2013-10-04 15:28:55.678 UTC promoter_file The file we provided as input with genomic information with a promoter region for each gene included. 2013-10-04 15:28:18.415 UTC p_value the pvalue indicating the significance of the kolmogorov smirnov test, between the two distributions of genes that overlap and the ones that do not overlap with the epigenetic file. 2013-11-02 14:03:02.455 UTC distance the distance D between the two distributions of genes that overlap and the ones that do not overlap with the epigenetic file. The greatest the difference the bigger the effect of the epigenetic file on the list of genes 2013-11-02 14:02:47.780 UTC ecdf_plot empirical cumulative distribution plot between the two distributions of genes that overlap and the ones that do not overlap with the epigenetic file under study. 2013-11-02 14:02:29.958 UTC calculate_promoter_regionupstream0downstream0overlap0gene_expr_file0epigenetic_file0gene_chr0inter_chr0inter_start0inter_end0genes_mapped0overlapping_genes_pvals_file00non_overlapping_genes_pvals_file00promoter_file00ks_D00ks_p00figure00 For each one of the genes we compute a promoter region according to the prespecified values of the variables upstream_bp and downstream_bp the transcription start site. In this component we take into account the direction that a gene is transcribed. Then the workflow computes overlaps between genes and the epigenetic file. The output of this process is two files. one that contains genes that overlap with the genomic region and another that does not overlap. 2013-10-04 15:44:39.344 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity genes_mapped 0 false upstream 0 false downstream 0 false epigenetic_file 0 false overlap 0 false gene_expr_file 0 false gene_chr 0 false inter_chr 0 false inter_start 0 false inter_end 0 false promoter_file 0 0 overlapping_genes_pvals_file 0 0 non_overlapping_genes_pvals_file 0 0 ks_D 0 0 ks_p 0 0 figure 0 0 false localhost 6311 true false genes_mapped TEXT_FILE upstream DOUBLE downstream DOUBLE epigenetic_file TEXT_FILE overlap INTEGER gene_expr_file TEXT_FILE gene_chr INTEGER inter_chr INTEGER inter_start INTEGER inter_end INTEGER promoter_file TEXT_FILE overlapping_genes_pvals_file TEXT_FILE non_overlapping_genes_pvals_file TEXT_FILE ks_D STRING ks_p STRING figure PNG_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecalculate_promoter_regionupstreamupstreamcalculate_promoter_regiondownstreamdownstreamcalculate_promoter_regionoverlapoverlapcalculate_promoter_regiongene_expr_filegene_expr_filecalculate_promoter_regionepigenetic_fileepigen_filecalculate_promoter_regiongene_chrgene_chrcalculate_promoter_regioninter_chrepigen_file_chrcalculate_promoter_regioninter_startepigen_file_startcalculate_promoter_regioninter_endepigen_file_endcalculate_promoter_regiongenes_mappedbiomartfilegenes_overlapcalculate_promoter_regionoverlapping_genes_pvals_filegenes_non_overlapcalculate_promoter_regionnon_overlapping_genes_pvals_filepromoter_filecalculate_promoter_regionpromoter_filep_valuecalculate_promoter_regionks_pdistancecalculate_promoter_regionks_Decdf_plotcalculate_promoter_regionfigure 8920e89b-959f-48dd-9031-f981efa7d034 2012-01-24 16:31:00.239 UTC b379ca3e-de58-4424-9fa4-fae883a0fadb 2012-04-13 17:12:21.129 UTC d071418e-3787-43fa-999b-b73c9e253299 2012-01-23 15:52:57.836 UTC b7cf6b39-08db-4073-916b-02909955df1a 2012-02-02 17:35:29.371 UTC b5f3c2eb-2443-4903-91f6-34ae14e16067 2012-07-17 10:29:04.194 UTC 45d35b25-d9b9-4f1c-bdf1-6186f12581b5 2012-02-03 17:49:12.70 UTC 7d3fcf98-1377-4b46-a614-1cbe98c80749 2012-04-11 10:56:40.674 UTC b911450a-2b57-4ba2-9e59-5767dbc52340 2011-12-27 13:09:07.542 UTC 6b6d0b1b-2872-4f3f-a993-83e424111537 2012-06-26 13:24:27.504 UTC 1e8a62a3-e59a-459a-bff9-b5b96cca60ac 2012-02-02 17:21:06.363 UTC 8f1eb77f-4480-4eac-8806-b225078b07cd 2012-10-25 12:38:43.625 UTC 812d2007-10f6-4cfc-acfe-6d4f0b657c1d 2012-02-02 17:28:41.67 UTC 7e2a5650-c14a-4d07-b871-141e3144f22b 2012-10-31 17:01:34.769 UTC get promoter region + operate on genomic intervals for T2WEB 2013-11-04 19:35:45.198 UTC 52fc7816-5044-4ac9-bb9f-c9b200998774 2012-01-23 16:05:10.564 UTC 204de4d5-a0fe-4b41-a1a2-a406650da0ff 2012-02-20 17:36:53.464 UTC 63e088eb-25a2-443d-8403-4a9e721de689 2012-02-21 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a8556ee4-8f90-4f72-898b-7c200904dd61 2011-12-27 15:01:41.691 UTC 2b1c20f3-f289-47fa-89ac-1e068becc190 2012-11-01 15:18:29.507 UTC 0a6a35c4-14d8-4d6d-acb7-90d58c08887c 2012-01-12 11:13:18.941 UTC 8812fd4f-16cb-4993-bbc6-b70919dcbb0f 2012-02-20 17:34:50.931 UTC db6f2115-3c7c-41b6-9e2a-0581df18e16f 2012-03-30 12:17:35.354 UTC 41f950a5-5224-4dd6-b417-56d8539bdb8d 2012-02-01 14:13:30.746 UTC 7ad9f2b6-290c-44e2-9da9-29a8a2f8a9f4 2012-02-13 15:44:00.401 UTC b663d0b0-2eaa-44b9-aacb-74fe8c8b3ac5 2012-02-22 09:15:25.675 UTC 2cb1bf88-6e89-4530-a18f-01e9d25b64a5 2011-12-27 12:52:28.909 UTC cf87ce3c-296b-4d65-8f3d-69513b11370f 2012-02-01 13:51:46.2 UTC 82a3afa6-6dca-43cf-82bf-721a7a84f391 2012-06-26 11:02:08.36 UTC c628b12a-1582-4312-bd3a-9c2d2fe5fb27 2012-02-02 17:18:18.707 UTC 5ef52112-7760-4e63-b764-ca3be4f48d80 2011-12-27 13:07:36.646 UTC cedbd55c-80fc-46f9-8dd8-89f3e7fd5ae1 2013-04-03 13:54:01.198 UTC 891b6cdc-dc22-4c54-8bf0-086b714f7d74 2013-10-14 12:51:42.670 UTC 722bc3d9-37d6-45cf-8c19-412f4fc5758a 2012-02-28 15:34:28.997 UTC beb43c3a-e838-43f5-a514-e815d141e15f 2012-04-13 17:19:26.975 UTC 68c14eed-9d28-4aab-8424-90230b61696a 2012-02-13 15:53:05.305 UTC 3261d1fb-636d-44e9-a9f1-17ad8d834738 2013-08-28 09:03:09.748 UTC d29e3c43-89a7-4f69-9aa4-3f28037f06a4 2012-03-29 15:14:12.890 UTC f04e7b22-95a1-4e5f-be81-48d863c939b9 2012-02-21 16:36:58.879 UTC 260d4b1e-f434-4299-bebd-22d34e5935b8 2012-01-23 16:02:06.108 UTC 3f81b0db-a19f-4649-829e-82686c8a7eba 2012-01-12 11:21:44.581 UTC fda84efe-edca-42d2-8ed8-593298b9a5c9 2012-02-13 14:18:03.31 UTC 1a443964-1717-4e7f-82a9-d873e4e413f6 2013-04-03 13:46:44.935 UTC dcc22d5b-3930-4668-9478-3012bea2a366 2012-02-02 17:34:24.347 UTC 85abaefb-8e01-423f-96bf-c92d8f9666bb 2012-02-02 17:17:22.796 UTC 058c43e3-6c81-48dc-af3d-ca236f99bc7c 2012-02-28 10:50:50.327 UTC d2ed7753-44bf-4d04-a8d6-2fa60ef24f7b 2013-10-02 14:55:45.672 UTC 3114af2c-76a7-44ee-b408-3bbc75b6a783 2012-01-23 15:53:14.364 UTC e82f5700-f8f0-422c-87d1-832369575c2d 2012-02-20 17:30:10.235 UTC 642c6178-0fd9-456d-9656-72f1a22970b5 2012-01-13 17:36:03.79 UTC e512c7c5-9482-425a-8301-7b927603eeba 2012-02-03 17:21:07.174 UTC 6e41b673-c397-4f4f-b689-b8953ed89784 2012-01-24 16:22:38.215 UTC f3530ab7-e6e4-4554-844c-8d332abe73ce 2012-02-21 16:33:59.561 UTC Eleni Mina 2012-04-11 16:32:02.799 UTC 34fabe58-7f07-4c8d-926b-c945ef44c7b1 2011-12-27 13:23:22.907 UTC 0972ec5d-598c-4b01-90d9-e9bab332d1bd 2012-02-02 17:13:40.807 UTC 18e34daf-3a1a-44b2-ba5b-b259b66a0f39 2011-12-27 14:43:56.451 UTC 27bb749e-42eb-4c7b-9cbd-fd59e9635249 2013-10-14 12:48:26.605 UTC 5ad91cb9-e33f-45e0-9234-371f74f07d35 2012-11-01 15:50:41.288 UTC e1816b7a-550b-4737-a0c1-b30830ce6f38 2012-07-17 10:07:49.459 UTC f638ecfd-2249-4846-ac00-4c06f261c50a 2012-01-12 13:02:25.594 UTC 13783e6f-158c-4c67-8bb3-25e8ab031eca 2012-02-13 14:37:01.713 UTC 1e284d4e-9674-4141-931b-b60d4906eb02 2012-01-12 13:03:56.394 UTC 52d1a2cb-0988-4ca0-b6ea-a6c23716e6d7 2013-08-28 09:35:22.269 UTC 51cb3289-3d36-4c34-ae2f-71cd8d2b3043 2013-10-03 14:58:20.688 UTC c782fbf5-9f10-4a4a-a6df-5b7fb60284e8 2011-12-27 13:14:43.342 UTC c9c89c36-6674-442d-9388-925e385f9d4f 2012-02-03 17:36:05.926 UTC 225c93de-b681-41af-8cf0-aef0eb685bc4 2013-10-14 12:26:10.568 UTC efcb3274-d43f-488f-a005-119cc5b4678b 2013-10-04 15:29:05.534 UTC d6469c0c-5727-4968-a7e6-cf1fa7da7299 2012-02-13 17:10:20.194 UTC d199baa0-9894-43d2-ac92-0093148ebea5 2012-01-12 13:32:11.334 UTC 4be113e7-51d0-4fe3-a3a7-31d588ba3053 2012-06-26 10:51:20.419 UTC 6f028619-4e11-4705-89f6-981ac163bf4d 2012-01-13 17:09:19.195 UTC 84e5bfec-edb4-4696-9014-0f3cf5df7087 2011-12-27 13:03:15.446 UTC c35ef4e7-6615-43e6-82f3-18a761fed07f 2012-06-26 13:12:05.545 UTC 9a00f918-5749-424d-8190-bcb248191efc 2012-11-01 15:24:49.332 UTC 1b578e4d-7179-4f56-ad42-c76101a2d566 2013-08-28 08:52:14.57 UTC da29dac2-1f24-4d12-b705-94d531da98ab 2012-02-13 15:46:03.929 UTC 8f4227d0-17f6-46b3-891f-366d014d001f 2012-01-30 16:53:58.322 UTC 04e84afa-48a7-4e00-b60d-44ed1b24ffa5 2013-10-15 17:27:21.382 UTC d8b0f482-6c1a-49a5-80b8-42abe993f671 2012-02-13 14:39:02.105 UTC 0876f58b-a7da-4aa1-a142-ef2618582a4f 2012-01-12 11:01:50.593 UTC 25696f94-ff52-462f-af5a-a08ce4765938 2011-12-27 12:35:58.10 UTC 3f00f3b9-c373-4fef-a0c5-2dc8e7ff1072 2012-02-20 14:12:53.78 UTC c00cae35-6fcb-4822-92bc-2ec2ecf34591 2012-02-21 16:35:59.278 UTC 6a72fb1b-48d4-4802-a340-e0d3e71c7e5f 2012-01-25 10:54:16.279 UTC c51d0cdb-1cd9-47f1-bb96-3f92a1a1bf34 2013-10-03 14:34:55.544 UTC 23d4c20c-4dcb-4152-b1e9-81399312bf6a 2012-01-12 09:50:17.281 UTC d9bf7500-7f13-40bc-9ba3-7930177b8119 2012-01-13 16:55:48.487 UTC 63d180ea-0136-4c1f-9888-9a6a924681b9 2011-12-27 14:29:39.750 UTC 13787be5-8ca5-4f0f-bdff-c579c5d087e5 2012-01-12 13:39:16.86 UTC c6f14b21-7054-4a62-b89d-7baefd9f9db5 2012-02-13 17:01:16.850 UTC 59323802-ac42-4e00-b18d-acecb4ce9c3f 2013-10-04 15:25:06.400 UTC 82113d85-312e-4836-b508-23218b23d7c8 2012-03-16 11:06:44.472 UTC f6c4949b-4409-4235-bd9f-11c97c0e963c 2012-02-02 16:58:18.555 UTC 1ff4b606-4034-47c5-a43a-7744280aaeef 2012-02-02 17:10:21.179 UTC 041a2c9c-d993-4a0b-bd9f-9fe0e59fff08 2012-10-25 13:38:19.768 UTC 14c581e8-63a8-4b45-8407-e28744aad932 2012-01-25 10:39:52.156 UTC e4033f84-bbf9-4a7e-b5af-44bc256b627c 2012-10-25 12:30:38.478 UTC 054f0b6e-437d-4e66-b52d-0d488a193bef 2012-02-03 17:09:05.902 UTC bd485756-6694-4c08-8c28-fa26915668a9 2012-01-12 10:13:52.925 UTC f4af484f-1311-4cbb-aee2-bba1678e996b 2012-02-21 16:39:00.934 UTC 09155b2c-6855-48db-bc4f-19c0859546ce 2012-02-02 17:18:13.827 UTC b29f339e-87f3-43ec-b6b1-edaa2367c7d6 2012-01-24 16:19:58.943 UTC f9d0d0ef-ed30-4c96-bd93-9e8fea91bc8c 2013-10-15 17:36:26.141 UTC 2af73ff3-4015-4cb1-a329-34f787e5a065 2012-01-12 10:13:43.197 UTC 3146a612-dcff-41e0-9938-a5e767dcd953 2012-01-12 11:20:15.157 UTC d64cb52e-6c01-4ab8-be7b-2d298600c382 2013-04-03 13:48:18.620 UTC aa84ebdb-b7db-4e3b-918d-eedf3aee09ff 2012-01-12 10:07:06.825 UTC 26a1e1ca-7b82-4b67-845a-550b042201fa 2013-10-03 14:59:29.812 UTC 38932f05-f7c0-498e-a400-58ca7073a4a7 2012-01-23 15:50:20.852 UTC 07a6869d-41a1-48eb-8e04-038626a08f01 2012-02-10 15:16:56.892 UTC ec2e4d41-373b-4700-ade0-978fc304d953 2012-03-23 15:43:37.562 UTC e7d6ce88-6450-4908-b6a7-caa2afc2bbf6 2012-02-28 11:33:44.873 UTC f6d525a7-e118-42ab-b057-eb5d1864965d 2011-12-27 14:56:03.171 UTC 25477b4d-b9e6-4068-a579-625fa1979820 2012-01-12 09:51:57.485 UTC df4522ee-e024-4b5d-905e-5dd7bfc4b894 2012-02-02 17:09:47.19 UTC b962fc7a-46e4-4400-9d15-4a28c1f90cb2 2012-01-12 13:33:04.134 UTC 7f3eed14-7777-46b9-a6e1-832e82fe3a00 2012-01-12 13:29:59.502 UTC a4e52bb6-edae-4367-8be5-1f82b1140270 2012-02-08 11:22:20.605 UTC 84ffec2d-2fc9-4405-be5c-a59b8ad331bc 2012-02-10 15:12:49.741 UTC 32339da4-6199-47a1-a985-f17f8cd18ebc 2012-01-12 13:16:17.990 UTC 315cbbb7-506e-46ff-a0c2-a76e1c3baff7 2012-05-01 15:50:23.92 UTC 7e21416e-eb1f-429d-b4c6-ee73ae8167a0 2012-01-23 15:44:59.412 UTC f17c610e-e3e4-4231-b2f5-286316290000 2012-01-13 17:42:31.191 UTC This workflow computes a promoter region for each gene that we provide as input carrying the genomic information. Then it computes the overlap between the two datasets that contain genomic information plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. Uses the R package GenomicRanges. 2013-10-04 15:30:51.910 UTC b3e6e773-31f3-42aa-a850-c67277219dd9 2011-12-27 12:25:06.468 UTC