[{"related_material":{"record":[{"relation":"used_in_publication","id":"9283","status":"public"}]},"doi":"10.15479/AT:ISTA:8951","ddc":["570"],"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:57Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","citation":{"chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","short":"A.A. Nagy-Staron, (2020).","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>"},"type":"research_data","author":[{"orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron"}],"has_accepted_license":"1","oa_version":"Published Version","year":"2020","day":"21","contributor":[{"contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron"},{"first_name":"Kathrin","last_name":"Tomasek","contributor_type":"project_member","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","last_name":"Caruso Carter","contributor_type":"project_member"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"last_name":"Kavcic","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","last_name":"Guet","first_name":"Calin C"}],"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-12-20T22:01:44Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","date_created":"2020-12-20T10:00:26Z","_id":"8951","date_published":"2020-12-21T00:00:00Z","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"month":"12","file":[{"content_type":"text/plain","file_id":"8952","relation":"main_file","success":1,"date_created":"2020-12-20T09:52:52Z","file_name":"readme.txt","creator":"bkavcic","file_size":523,"date_updated":"2020-12-20T09:52:52Z","access_level":"open_access","checksum":"f57862aeee1690c7effd2b1117d40ed1"},{"file_name":"GRNs Research depository.gb","file_size":379228,"creator":"bkavcic","date_updated":"2020-12-20T22:01:44Z","access_level":"open_access","checksum":"f2c6d5232ec6d551b6993991e8689e9f","content_type":"application/octet-stream","relation":"main_file","file_id":"8954","success":1,"date_created":"2020-12-20T22:01:44Z"}]},{"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","citation":{"ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>.","mla":"Vicoso, Beatriz. <i>Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018)</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","short":"B. Vicoso, (2018).","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>"},"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"type":"research_data","has_accepted_license":"1","oa_version":"Published Version","year":"2018","contributor":[{"first_name":"Marion A","last_name":"Picard","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"day":"24","related_material":{"record":[{"relation":"research_paper","id":"131","status":"public"}]},"project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"datarep_id":"109","doi":"10.15479/AT:ISTA:109","ddc":["570"],"keyword":["schistosoma","Z-chromosome","gene expression"],"date_updated":"2024-02-21T13:45:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_published":"2018-07-24T00:00:00Z","_id":"5586","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"date_created":"2018-12-12T12:31:40Z","month":"07","file":[{"date_created":"2018-12-12T13:02:35Z","content_type":"application/zip","relation":"main_file","file_id":"5601","checksum":"e60b484bd6f55c08eb66a189cb72c923","date_updated":"2020-07-14T12:47:08Z","access_level":"open_access","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","creator":"system","file_size":11918144}],"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:08Z"},{"related_material":{"record":[{"relation":"research_paper","id":"6089","status":"public"}]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.15479/at:ista:/5757","ddc":["576"],"date_updated":"2024-02-21T13:59:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","ec_funded":1,"citation":{"chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","short":"C. Fraisse, (2018).","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>"},"year":"2018","has_accepted_license":"1","oa_version":"Published Version","author":[{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","day":"19","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"article_processing_charge":"No","_id":"5757","date_published":"2018-12-19T00:00:00Z","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"date_created":"2018-12-19T14:22:35Z","file":[{"content_type":"application/zip","relation":"main_file","file_id":"5758","date_created":"2018-12-19T14:19:52Z","file_name":"FileS1.zip","creator":"cfraisse","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd"},{"file_name":"FileS2.zip","file_size":84856909,"creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","content_type":"application/zip","file_id":"5759","relation":"main_file","date_created":"2018-12-19T14:19:49Z"},{"date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","relation":"main_file","file_id":"5760","checksum":"c37ac5d5437c457338afc128c1240655","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","file_name":"FileS3.txt","file_size":881133,"creator":"cfraisse"},{"access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9","creator":"cfraisse","file_size":883742,"file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_id":"5761","content_type":"text/plain"},{"content_type":"text/plain","file_id":"5762","relation":"main_file","date_created":"2018-12-19T14:19:49Z","file_name":"FileS5.txt","file_size":2495437,"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_name":"FileS6.txt","file_size":15913457,"creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","content_type":"text/plain","file_id":"5763","relation":"main_file"},{"creator":"cfraisse","file_size":2584120,"file_name":"FileS7.txt","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","file_id":"5764","relation":"main_file","content_type":"text/plain","date_created":"2018-12-19T14:19:50Z"},{"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"creator":"cfraisse","file_name":"FileS8.txt","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_id":"5765","content_type":"text/plain"},{"content_type":"text/plain","relation":"main_file","file_id":"5766","date_created":"2018-12-19T14:19:50Z","file_name":"FileS9.txt","creator":"cfraisse","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae"}],"month":"12"}]