Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms...
Gespeichert in:
| Hauptverfasser: | , , , , , , , , |
|---|---|
| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
10 November 2023
|
| In: |
Nucleic acids research
Year: 2023, Jahrgang: 51, Heft: 20, Pages: 10934-10949 |
| ISSN: | 1362-4962 |
| DOI: | 10.1093/nar/gkad841 |
| Online-Zugang: | Verlag, kostenfrei, Volltext: https://doi.org/10.1093/nar/gkad841
|
| Verfasserangaben: | Sophia Müller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O. Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Dénes Türei, Astrid Lægreid and Julio Saez-Rodriguez |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1871946468 | ||
| 003 | DE-627 | ||
| 005 | 20240307034941.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231205s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1093/nar/gkad841 |2 doi | |
| 035 | |a (DE-627)1871946468 | ||
| 035 | |a (DE-599)KXP1871946468 | ||
| 035 | |a (OCoLC)1425209010 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 32 |2 sdnb | ||
| 100 | 1 | |a Müller-Dott, Sophia |d 1997- |e VerfasserIn |0 (DE-588)1285035623 |0 (DE-627)1840945710 |4 aut | |
| 245 | 1 | 0 | |a Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities |c Sophia Müller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O. Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Dénes Türei, Astrid Lægreid and Julio Saez-Rodriguez |
| 264 | 1 | |c 10 November 2023 | |
| 300 | |b Illustrationen | ||
| 300 | |a 16 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Online verfügbar: 16. Oktober 2023 | ||
| 500 | |a Gesehen am 05.12.2023 | ||
| 520 | |a Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1186 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by examining TF activity profiles in three different cancer types and exploring TF activities at the level of single-cells. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data. | ||
| 700 | 1 | |a Tsirvouli, Eirini |e VerfasserIn |4 aut | |
| 700 | 1 | |a Vazquez, Miguel |e VerfasserIn |4 aut | |
| 700 | 1 | |a Ramirez Flores, Ricardo O. |e VerfasserIn |0 (DE-588)1233991973 |0 (DE-627)1758398167 |4 aut | |
| 700 | 1 | |a Badia-i-Mompel, Pau |d 1996- |e VerfasserIn |0 (DE-588)1261665708 |0 (DE-627)1808807987 |4 aut | |
| 700 | 1 | |a Fallegger, Robin |e VerfasserIn |0 (DE-588)131221631X |0 (DE-627)1871978939 |4 aut | |
| 700 | 1 | |a Türei, Dénes |e VerfasserIn |0 (DE-588)1235344592 |0 (DE-627)176038478X |4 aut | |
| 700 | 1 | |a Lægreid, Astrid |e VerfasserIn |4 aut | |
| 700 | 1 | |a Sáez Rodríguez, Julio |d 1978- |e VerfasserIn |0 (DE-588)133764362 |0 (DE-627)555766632 |0 (DE-576)300083114 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Nucleic acids research |d Oxford : Oxford Univ. Press, 1974 |g 51(2023), 20, Seite 10934-10949 |h Online-Ressource |w (DE-627)26813250X |w (DE-600)1472175-2 |w (DE-576)07760878X |x 1362-4962 |7 nnas |a Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities |
| 773 | 1 | 8 | |g volume:51 |g year:2023 |g number:20 |g pages:10934-10949 |g extent:16 |a Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities |
| 856 | 4 | 0 | |u https://doi.org/10.1093/nar/gkad841 |x Verlag |x Resolving-System |z kostenfrei |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20231205 | ||
| 993 | |a Article | ||
| 994 | |a 2023 | ||
| 998 | |g 133764362 |a Sáez Rodríguez, Julio |m 133764362:Sáez Rodríguez, Julio |d 910000 |d 912900 |e 910000PS133764362 |e 912900PS133764362 |k 0/910000/ |k 1/910000/912900/ |p 9 |y j | ||
| 998 | |g 1235344592 |a Türei, Dénes |m 1235344592:Türei, Dénes |d 910000 |d 912900 |d 700000 |d 716000 |e 910000PT1235344592 |e 912900PT1235344592 |e 700000PT1235344592 |e 716000PT1235344592 |k 0/910000/ |k 1/910000/912900/ |k 0/700000/ |k 1/700000/716000/ |p 7 | ||
| 998 | |g 131221631X |a Fallegger, Robin |m 131221631X:Fallegger, Robin |d 910000 |d 912900 |e 910000PF131221631X |e 912900PF131221631X |k 0/910000/ |k 1/910000/912900/ |p 6 | ||
| 998 | |g 1261665708 |a Badia-i-Mompel, Pau |m 1261665708:Badia-i-Mompel, Pau |d 910000 |d 912900 |e 910000PB1261665708 |e 912900PB1261665708 |k 0/910000/ |k 1/910000/912900/ |p 5 | ||
| 998 | |g 1233991973 |a Ramirez Flores, Ricardo O. |m 1233991973:Ramirez Flores, Ricardo O. |d 910000 |d 912900 |e 910000PR1233991973 |e 912900PR1233991973 |k 0/910000/ |k 1/910000/912900/ |p 4 | ||
| 998 | |g 1285035623 |a Müller-Dott, Sophia |m 1285035623:Müller-Dott, Sophia |d 910000 |d 912900 |e 910000PM1285035623 |e 912900PM1285035623 |k 0/910000/ |k 1/910000/912900/ |p 1 |x j | ||
| 999 | |a KXP-PPN1871946468 |e 442552988X | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"type":{"media":"Online-Ressource","bibl":"article-journal"},"note":["Online verfügbar: 16. Oktober 2023","Gesehen am 05.12.2023"],"origin":[{"dateIssuedDisp":"10 November 2023","dateIssuedKey":"2023"}],"title":[{"title_sort":"Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities","title":"Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities"}],"id":{"doi":["10.1093/nar/gkad841"],"eki":["1871946468"]},"name":{"displayForm":["Sophia Müller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O. Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Dénes Türei, Astrid Lægreid and Julio Saez-Rodriguez"]},"physDesc":[{"extent":"16 S.","noteIll":"Illustrationen"}],"relHost":[{"language":["eng"],"titleAlt":[{"title":"NAR online"},{"title":"NAR"},{"title":"Database issue"},{"title":"Web server issue"}],"part":{"text":"51(2023), 20, Seite 10934-10949","issue":"20","pages":"10934-10949","year":"2023","extent":"16","volume":"51"},"physDesc":[{"extent":"Online-Ressource"}],"recId":"26813250X","id":{"eki":["26813250X"],"zdb":["1472175-2"],"issn":["1362-4962"]},"title":[{"title":"Nucleic acids research","title_sort":"Nucleic acids research"}],"origin":[{"publisherPlace":"Oxford","dateIssuedDisp":"1974-","publisher":"Oxford Univ. Press","dateIssuedKey":"1974"}],"note":["Gesehen am 15.09.2025","Ungezählte Beil.: Database issue; Web server issue"],"pubHistory":["1.1974 -"],"disp":"Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activitiesNucleic acids research","type":{"bibl":"periodical","media":"Online-Ressource"}}],"recId":"1871946468","person":[{"display":"Müller-Dott, Sophia","family":"Müller-Dott","role":"aut","given":"Sophia"},{"role":"aut","given":"Eirini","display":"Tsirvouli, Eirini","family":"Tsirvouli"},{"given":"Miguel","role":"aut","family":"Vazquez","display":"Vazquez, Miguel"},{"given":"Ricardo O.","role":"aut","family":"Ramirez Flores","display":"Ramirez Flores, Ricardo O."},{"display":"Badia-i-Mompel, Pau","family":"Badia-i-Mompel","role":"aut","given":"Pau"},{"family":"Fallegger","display":"Fallegger, Robin","role":"aut","given":"Robin"},{"role":"aut","given":"Dénes","family":"Türei","display":"Türei, Dénes"},{"display":"Lægreid, Astrid","family":"Lægreid","role":"aut","given":"Astrid"},{"display":"Sáez Rodríguez, Julio","family":"Sáez Rodríguez","role":"aut","given":"Julio"}],"language":["eng"]} | ||
| SRT | |a MUELLERDOTEXPANDINGT1020 | ||