FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4311593295> ?p ?o ?g. }

• W4311593295 abstract "Abstract Motivation gene co-expression networks have been widely applied to identify critical genes and pathways for neurodegenerative diseases such as Parkinson’s and Alzheimer’s disease. Now, with the advent of single-cell RNA-sequencing, we have the opportunity to create cell-type specific gene co-expression networks. However, single-cell RNA-sequencing data is characterized by its sparsity, amongst some other issues raised by this new type of data. Results We present scCoExpNets, a framework for the discovery and analysis of cell-type specific gene coexpression networks (GCNs) from single-cell RNA-seq data. We propose a new strategy to address the problem of sparsity, named iterative pseudo-cell identification. It consists of adding the gene expression of pairs of cells that belong to the same individual and the same cell-type while the number of cells is over 200, thus creating multiple matrices and multiple scGCNs for the same cell-type, all of them seen as alternative and complementary views of the same phenomena. We applied this new tool on a snRNA-seq dataset human post-mortem substantia nigra pars compacta tissue of 13 controls and 14 Parkinson’s disease (PD) cases (18 males and 9 females) with 30-99 years. We show that one of the hypotheses that support the selective vulnerability of dopaminergic neurons in PD, the iron accumulation, is sustained in our dopaminergic neurons network models. Moreover, after successive pseudo-celluling iterations, the gene groups sustaining this hypothesis remain intact. At the same time, this pseudo-celulling strategy also allows us to discover genes whose grouping changes considerably throughout the iterations and provides new insights. Finally, since some of our models were correlated with diagnosis and age at the same time, we also developed our own framework to create covariate-specific GCNs, called CovCoExpNets. We applied this new software to our snRNA-seq dataset and we identified 11 age-specific genes and 5 diagnosis-specific genes which do not overlap. Availability and implementation The CoExpNets implementations are available as R packages: scCoExpNets for creating single-cell GCNs and CovCoExpNets for creating covariate-specific GCNs. Users can either download the development version via github https://github.com/aliciagp/scCoExpNets and https://github.com/aliciagp/CovCoExpNets Contact alicia.gomez1@um.es Supplementary information supplementary data is available online." @default.
• W4311593295 created "2022-12-27" @default.
• W4311593295 creator A5004678592 @default.
• W4311593295 creator A5015059988 @default.
• W4311593295 creator A5037468303 @default.
• W4311593295 creator A5042646713 @default.
• W4311593295 creator A5045954437 @default.
• W4311593295 creator A5046504926 @default.
• W4311593295 creator A5051204041 @default.
• W4311593295 creator A5052463742 @default.
• W4311593295 creator A5052933090 @default.
• W4311593295 creator A5055155669 @default.
• W4311593295 creator A5059061235 @default.
• W4311593295 creator A5062444315 @default.
• W4311593295 creator A5064977245 @default.
• W4311593295 creator A5076611003 @default.
• W4311593295 creator A5086627945 @default.
• W4311593295 date "2022-12-15" @default.
• W4311593295 modified "2023-10-15" @default.
• W4311593295 title "Single-nucleus co-expression networks of dopaminergic neurons support iron accumulation as a plausible explanation to their vulnerability in Parkinson’s disease" @default.
• W4311593295 cites W1498383300 @default.
• W4311593295 cites W1644155731 @default.
• W4311593295 cites W1698967089 @default.
• W4311593295 cites W1966327575 @default.
• W4311593295 cites W1974033269 @default.
• W4311593295 cites W1997012068 @default.
• W4311593295 cites W1997183854 @default.
• W4311593295 cites W2019035911 @default.
• W4311593295 cites W2024173595 @default.
• W4311593295 cites W2048086807 @default.
• W4311593295 cites W2056413798 @default.
• W4311593295 cites W2056516296 @default.
• W4311593295 cites W2086277161 @default.
• W4311593295 cites W2093731271 @default.
• W4311593295 cites W2100759421 @default.
• W4311593295 cites W2104719009 @default.
• W4311593295 cites W2107473715 @default.
• W4311593295 cites W2112455323 @default.
• W4311593295 cites W2112867510 @default.
• W4311593295 cites W2134412560 @default.
• W4311593295 cites W2141525353 @default.
• W4311593295 cites W2142430469 @default.
• W4311593295 cites W2150634893 @default.
• W4311593295 cites W2169353806 @default.
• W4311593295 cites W2279488356 @default.
• W4311593295 cites W2315662623 @default.
• W4311593295 cites W2339552778 @default.
• W4311593295 cites W2341840009 @default.
• W4311593295 cites W2374069442 @default.
• W4311593295 cites W2479861806 @default.
• W4311593295 cites W2528543174 @default.
• W4311593295 cites W2555006703 @default.
• W4311593295 cites W2572710398 @default.
• W4311593295 cites W2583594489 @default.
• W4311593295 cites W2603409591 @default.
• W4311593295 cites W2606575226 @default.
• W4311593295 cites W2623843598 @default.
• W4311593295 cites W2726542547 @default.
• W4311593295 cites W2746479894 @default.
• W4311593295 cites W2771043801 @default.
• W4311593295 cites W2791786275 @default.
• W4311593295 cites W2792510508 @default.
• W4311593295 cites W2806614570 @default.
• W4311593295 cites W2883210621 @default.
• W4311593295 cites W2884263697 @default.
• W4311593295 cites W2890004445 @default.
• W4311593295 cites W2898371604 @default.
• W4311593295 cites W2912119914 @default.
• W4311593295 cites W2942678593 @default.
• W4311593295 cites W2949177718 @default.
• W4311593295 cites W2951506174 @default.
• W4311593295 cites W2952673268 @default.
• W4311593295 cites W2958337029 @default.
• W4311593295 cites W2970899415 @default.
• W4311593295 cites W2972368830 @default.
• W4311593295 cites W2972937106 @default.
• W4311593295 cites W2986932567 @default.
• W4311593295 cites W2989971001 @default.
• W4311593295 cites W3009609875 @default.
• W4311593295 cites W3015873948 @default.
• W4311593295 cites W3019480645 @default.
• W4311593295 cites W3019747475 @default.
• W4311593295 cites W3022457072 @default.
• W4311593295 cites W3042896257 @default.
• W4311593295 cites W3044920485 @default.
• W4311593295 cites W3065451431 @default.
• W4311593295 cites W3080632072 @default.
• W4311593295 cites W3092754274 @default.
• W4311593295 cites W3099862724 @default.
• W4311593295 cites W3128690417 @default.
• W4311593295 cites W3132131821 @default.
• W4311593295 cites W3133590080 @default.
• W4311593295 cites W3137732484 @default.
• W4311593295 cites W3157419554 @default.
• W4311593295 cites W3170996424 @default.
• W4311593295 cites W3173999512 @default.
• W4311593295 cites W3177149152 @default.
• W4311593295 cites W3179493165 @default.
• W4311593295 cites W3179788429 @default.
• W4311593295 cites W3180268318 @default.

• next