Sökning: onr:"swepub:oai:research.chalmers.se:236d605b-a94b-42f0-aa6a-0e4e6aebd2ce" > Generation and anal...
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000 | 04870naa a2200553 4500 | |
001 | oai:research.chalmers.se:236d605b-a94b-42f0-aa6a-0e4e6aebd2ce | |
003 | SwePub | |
008 | 230210s2023 | |||||||||||000 ||eng| | |
009 | oai:gup.ub.gu.se/330092 | |
024 | 7 | a https://doi.org/10.1073/pnas.22178681202 DOI |
024 | 7 | a https://research.chalmers.se/publication/5345462 URI |
024 | 7 | a https://gup.ub.gu.se/publication/3300922 URI |
040 | a (SwePub)cthd (SwePub)gu | |
041 | a engb eng | |
042 | 9 SwePub | |
072 | 7 | a art2 swepub-publicationtype |
072 | 7 | a ref2 swepub-contenttype |
100 | 1 | a Gustafsson, Johan,d 1976u Chalmers tekniska högskola,Chalmers University of Technology4 aut0 (Swepub:cth)gustajo |
245 | 1 0 | a Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data |
264 | c 2023-01-31 | |
264 | 1 | b Proceedings of the National Academy of Sciences,c 2023 |
338 | a electronic2 rdacarrier | |
520 | a Single-cell RNA sequencing combined with genome-scale metabolic models (GEMs) has the potential to unravel the differences in metabolism across both cell types and cell states but requires new computational methods. Here, we present a method for generating cell-type-specific genome-scale models from clusters of single-cell RNA-Seq profiles. Specifically, we developed a method to estimate the minimum number of cells required to pool to obtain stable models, a bootstrapping strategy for estimating statistical inference, and a faster version of the task-driven integrative network inference for tissues algorithm for generating context-specific GEMs. In addition, we evaluated the effect of different RNA-Seq normalization methods on model topology and differences in models generated from single-cell and bulk RNA-Seq data. We applied our methods on data from mouse cortex neurons and cells from the tumor microenvironment of lung cancer and in both cases found that almost every cell subtype had a unique metabolic profile. In addition, our approach was able to detect cancer-associated metabolic differences between cancer cells and healthy cells, showcasing its utility. We also contextualized models from 202 single-cell clusters across 19 human organs using data from Human Protein Atlas and made these available in the web portal Metabolic Atlas, thereby providing a valuable resource to the scientific community. With the ever-increasing availability of single-cell RNA-Seq datasets and continuously improved GEMs, their combination holds promise to become an important approach in the study of human metabolism. | |
650 | 7 | a NATURVETENSKAPx Biologix Cellbiologi0 (SwePub)106042 hsv//swe |
650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Cell Biology0 (SwePub)106042 hsv//eng |
650 | 7 | a NATURVETENSKAPx Data- och informationsvetenskapx Bioinformatik0 (SwePub)102032 hsv//swe |
650 | 7 | a NATURAL SCIENCESx Computer and Information Sciencesx Bioinformatics0 (SwePub)102032 hsv//eng |
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 |
653 | a RNA-Seq | |
653 | a GEM | |
653 | a modeling | |
653 | a single-cell | |
653 | a GEM | |
653 | a single-cell | |
653 | a RNA-Seq | |
653 | a modeling | |
700 | 1 | a Anton, Petre Mihail,d 1989u Chalmers tekniska högskola,Chalmers University of Technology4 aut0 (Swepub:cth)petre |
700 | 1 | a Roshanzamir, Fariba,d 1986u Chalmers tekniska högskola,Chalmers University of Technology4 aut0 (Swepub:cth)faribar |
700 | 1 | a Jörnsten, Rebecka,d 1971u Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences4 aut0 (Swepub:cth)jornsten |
700 | 1 | a Kerkhoven, Eduard,d 1985u Chalmers tekniska högskola,Chalmers University of Technology4 aut0 (Swepub:cth)eduardk |
700 | 1 | a Robinson, Jonathan,d 1986u Chalmers tekniska högskola,Chalmers University of Technology,BioInnovation Institute (BII)4 aut0 (Swepub:cth)jonrob |
700 | 1 | a Nielsen, Jens B,d 1962u BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology4 aut0 (Swepub:cth)nielsenj |
710 | 2 | a Chalmers tekniska högskolab Institutionen för matematiska vetenskaper4 org |
773 | 0 | t Proceedings of the National Academy of Sciences of the United States of Americad : Proceedings of the National Academy of Sciencesg 120:6q 120:6x 0027-8424x 1091-6490 |
856 | 4 | u https://research.chalmers.se/publication/534546/file/534546_Fulltext.pdfx primaryx freey FULLTEXT |
856 | 4 8 | u https://doi.org/10.1073/pnas.2217868120 |
856 | 4 8 | u https://research.chalmers.se/publication/534546 |
856 | 4 8 | u https://gup.ub.gu.se/publication/330092 |
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