id:"swepub:oai:DiVA.org:his-20941"
Sökning: id:"swepub:oai:DiVA.org:his-20941" > Deep neural network...
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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 05503naa a2200529 4500 | |
| 001 | oai:DiVA.org:his-20941 | |
| 003 | SwePub | |
| 008 | 220225s2022 | |||||||||||000 ||eng| | |
| 009 | oai:DiVA.org:liu-183400 | |
| 009 | oai:prod.swepub.kib.ki.se:148910137 | |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-209412 URI |
| 024 | 7 | a https://doi.org/10.1038/s41540-022-00218-92 DOI |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-1834002 URI |
| 024 | 7 | a http://kipublications.ki.se/Default.aspx?queryparsed=id:1489101372 URI |
| 040 | a (SwePub)hisd (SwePub)liud (SwePub)ki | |
| 041 | a engb eng | |
| 042 | 9 SwePub | |
| 072 | 7 | a ref2 swepub-contenttype |
| 072 | 7 | a art2 swepub-publicationtype |
| 100 | 1 | a Magnusson, Rasmus,d 1992-u Linköpings universitet,Högskolan i Skövde,Institutionen för biovetenskap,Forskningsmiljön Systembiologi,Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Sweden,Translational Bioinformatics,Avdelningen för medicinsk teknik,Tekniska fakulteten,Univ Skovde, Sweden4 aut0 (Swepub:liu)rasma87 |
| 245 | 1 0 | a Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box |
| 264 | c 2022-02-23 | |
| 264 | 1 | b Springer Nature,c 2022 |
| 338 | a electronic2 rdacarrier | |
| 500 | a CC BY 4.0Correspondence and requests for materials should be addressed to Rasmus Magnusson email: rasmus.magnusson@his.seOpen access funding provided by University of Skövde. | |
| 500 | a Funding Agencies|Swedish Research CouncilSwedish Research CouncilEuropean Commission [2019-04193]; Swedish foundation for strategic researchSwedish Foundation for Strategic Research [SB16-0095]; Center for Industrial IT (CENIIT); Systems Biology Research Centre at University of Skovde under Knowledge Foundation [20200014]; King Abdullah University of Science and Technology (KAUST)King Abdullah University of Science & Technology; Swedish National Infrastructure for Computing (SNIC) [SNIC 2020/5-177, LiU-2019-25] | |
| 520 | a Prediction algorithms for protein or gene structures, including transcription factor binding from sequence information, have been transformative in understanding gene regulation. Here we ask whether human transcriptomic profiles can be predicted solely from the expression of transcription factors (TFs). We find that the expression of 1600 TFs can explain >95% of the variance in 25,000 genes. Using the light-up technique to inspect the trained NN, we find an over-representation of known TF-gene regulations. Furthermore, the learned prediction network has a hierarchical organization. A smaller set of around 125 core TFs could explain close to 80% of the variance. Interestingly, reducing the number of TFs below 500 induces a rapid decline in prediction performance. Next, we evaluated the prediction model using transcriptional data from 22 human diseases. The TFs were sufficient to predict the dysregulation of the target genes (rho = 0.61, P < 10−216). By inspecting the model, key causative TFs could be extracted for subsequent validation using disease-associated genetic variants. We demonstrate a methodology for constructing an interpretable neural network predictor, where analyses of the predictors identified key TFs that were inducing transcriptional changes during disease. | |
| 650 | 7 | a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng |
| 650 | 7 | a NATURVETENSKAPx Biologix Genetik0 (SwePub)106092 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Genetics0 (SwePub)106092 hsv//eng |
| 650 | 7 | a NATURVETENSKAPx Biologix Biokemi och molekylärbiologi0 (SwePub)106022 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Biochemistry and Molecular Biology0 (SwePub)106022 hsv//eng |
| 653 | a Bioinformatik | |
| 653 | a Bioinformatics | |
| 700 | 1 | a Tegnér, Jesper N.u Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia ; Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ; Science for Life Laboratory, Solna, Sweden,King Abdullah Univ Sci & Technol KAUST, Saudi Arabia; Dept Med, Sweden; Karolinska Inst, Sweden; Sci Life Lab, Sweden4 aut |
| 700 | 1 | a Gustafsson, Mikau Linköpings universitet,Bioinformatik,Tekniska fakulteten4 aut0 (Swepub:liu)mikgu75 |
| 710 | 2 | a Högskolan i Skövdeb Institutionen för biovetenskap4 org |
| 773 | 0 | t npj Systems Biology and Applicationsd : Springer Natureg 8:1q 8:1x 2056-7189 |
| 856 | 4 | u https://doi.org/10.1038/s41540-022-00218-9y Fulltext |
| 856 | 4 | u https://his.diva-portal.org/smash/get/diva2:1640666/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print |
| 856 | 4 | u https://www.nature.com/articles/s41540-022-00218-9.pdf |
| 856 | 4 | u https://liu.diva-portal.org/smash/get/diva2:1643530/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20941 |
| 856 | 4 8 | u https://doi.org/10.1038/s41540-022-00218-9 |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-183400 |
| 856 | 4 8 | u http://kipublications.ki.se/Default.aspx?queryparsed=id:148910137 |
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