Cover Image

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited th...

Full description

Saved in:
Bibliographic Details
Main Authors: Tanevski, Jovan (Author) , Nguyen, Thin (Author) , Truong, Buu (Author) , Karaiskos, Nikos (Author) , Ahsen, Mehmet Eren (Author) , Zhang, Xinyu (Author) , Shu, Chang (Author) , Xu, Ke (Author) , Liang, Xiaoyu (Author) , Hu, Ying (Author) , Pham, Hoang VV (Author) , Xiaomei, Li (Author) , Le, Thuc D. (Author) , Tarca, Adi L. (Author) , Bhatti, Gaurav (Author) , Romero, Roberto (Author) , Karathanasis, Nestoras (Author) , Loher, Phillipe (Author) , Chen, Yang (Author) , Ouyang, Zhengqing (Author) , Mao, Disheng (Author) , Zhang, Yuping (Author) , Zand, Maryam (Author) , Ruan, Jianhua (Author) , Hafemeister, Christoph (Author) , Qiu, Peng (Author) , Tran, Duc (Author) , Nguyen, Tin (Author) , Gabor, Attila (Author) , Yu, Thomas (Author) , Guinney, Justin (Author) , Glaab, Enrico (Author) , Krause, Roland (Author) , Banda, Peter (Author) , Consortium, Dream Sctc (Author) , Stolovitzky, Gustavo (Author) , Rajewsky, Nikolaus (Author) , Sáez Rodríguez, Julio (Author) , Meyer, Pablo (Author)
Format: Article (Journal)
Language:English
Published: 24 September, 2020
In: Life science alliance
Year: 2020, Volume: 3, Issue: 11, Pages: 1-13
ISSN:2575-1077
DOI:10.26508/lsa.202000867
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.26508/lsa.202000867
Verlag, lizenzpflichtig, Volltext: https://www.life-science-alliance.org/content/3/11/e202000867
Get full text
Author Notes:Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang VV Pham, Li Xiaomei, Thuc D. Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Dream Sctc Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer

MARC

LEADER 00000caa a2200000 c 4500
001 1750041030
003 DE-627
005 20220819122838.0
007 cr uuu---uuuuu
008 210301s2020 xx |||||o 00| ||eng c
024 7 |a 10.26508/lsa.202000867  |2 doi 
035 |a (DE-627)1750041030 
035 |a (DE-599)KXP1750041030 
035 |a (OCoLC)1341396464 
040 |a DE-627  |b ger  |c DE-627  |e rda 
041 |a eng 
084 |a 33  |2 sdnb 
100 1 |a Tanevski, Jovan  |e VerfasserIn  |0 (DE-588)1207478083  |0 (DE-627)1693809079  |4 aut 
245 1 0 |a Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data  |c Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang VV Pham, Li Xiaomei, Thuc D. Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Dream Sctc Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer 
264 1 |c 24 September, 2020 
300 |a 13 
336 |a Text  |b txt  |2 rdacontent 
337 |a Computermedien  |b c  |2 rdamedia 
338 |a Online-Ressource  |b cr  |2 rdacarrier 
500 |a Gesehen am 01.03.2020 
520 |a Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the top 10 methods to a zebra fish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues. 
700 1 |a Nguyen, Thin  |e VerfasserIn  |4 aut 
700 1 |a Truong, Buu  |e VerfasserIn  |4 aut 
700 1 |a Karaiskos, Nikos  |e VerfasserIn  |4 aut 
700 1 |a Ahsen, Mehmet Eren  |e VerfasserIn  |4 aut 
700 1 |a Zhang, Xinyu  |e VerfasserIn  |4 aut 
700 1 |a Shu, Chang  |e VerfasserIn  |4 aut 
700 1 |a Xu, Ke  |e VerfasserIn  |4 aut 
700 1 |a Liang, Xiaoyu  |e VerfasserIn  |4 aut 
700 1 |a Hu, Ying  |e VerfasserIn  |4 aut 
700 1 |a Pham, Hoang VV  |e VerfasserIn  |4 aut 
700 1 |a Xiaomei, Li  |e VerfasserIn  |4 aut 
700 1 |a Le, Thuc D.  |e VerfasserIn  |4 aut 
700 1 |a Tarca, Adi L.  |e VerfasserIn  |4 aut 
700 1 |a Bhatti, Gaurav  |e VerfasserIn  |4 aut 
700 1 |a Romero, Roberto  |e VerfasserIn  |4 aut 
700 1 |a Karathanasis, Nestoras  |e VerfasserIn  |4 aut 
700 1 |a Loher, Phillipe  |e VerfasserIn  |4 aut 
700 1 |a Chen, Yang  |e VerfasserIn  |4 aut 
700 1 |a Ouyang, Zhengqing  |e VerfasserIn  |4 aut 
700 1 |a Mao, Disheng  |e VerfasserIn  |4 aut 
700 1 |a Zhang, Yuping  |e VerfasserIn  |4 aut 
700 1 |a Zand, Maryam  |e VerfasserIn  |4 aut 
700 1 |a Ruan, Jianhua  |e VerfasserIn  |4 aut 
700 1 |a Hafemeister, Christoph  |e VerfasserIn  |4 aut 
700 1 |a Qiu, Peng  |e VerfasserIn  |4 aut 
700 1 |a Tran, Duc  |e VerfasserIn  |4 aut 
700 1 |a Nguyen, Tin  |e VerfasserIn  |4 aut 
700 1 |a Gabor, Attila  |e VerfasserIn  |0 (DE-588)1226773125  |0 (DE-627)1747798843  |4 aut 
700 1 |a Yu, Thomas  |e VerfasserIn  |4 aut 
700 1 |a Guinney, Justin  |e VerfasserIn  |4 aut 
700 1 |a Glaab, Enrico  |e VerfasserIn  |4 aut 
700 1 |a Krause, Roland  |e VerfasserIn  |4 aut 
700 1 |a Banda, Peter  |e VerfasserIn  |4 aut 
700 1 |a Consortium, Dream Sctc  |e VerfasserIn  |4 aut 
700 1 |a Stolovitzky, Gustavo  |e VerfasserIn  |4 aut 
700 1 |a Rajewsky, Nikolaus  |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 
700 1 |a Meyer, Pablo  |e VerfasserIn  |4 aut 
773 0 8 |i Enthalten in  |t Life science alliance  |d Heidelberg : EMBO Press, 2018  |g 3(2020,11) Artikel-Nummer 202000867, 13 Seiten  |h Online-Ressource  |w (DE-627)1040376843  |w (DE-600)2948687-7  |w (DE-576)513597522  |x 2575-1077  |7 nnas  |a Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data 
773 1 8 |g volume:3  |g year:2020  |g number:11  |g pages:1-13  |g extent:13  |a Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data 
856 4 0 |u https://doi.org/10.26508/lsa.202000867  |x Verlag  |x Resolving-System  |z lizenzpflichtig  |3 Volltext 
856 4 0 |u https://www.life-science-alliance.org/content/3/11/e202000867  |x Verlag  |z lizenzpflichtig  |3 Volltext 
951 |a AR 
992 |a 20210301 
993 |a Article 
994 |a 2020 
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 38  |y j 
998 |g 1226773125  |a Gabor, Attila  |m 1226773125:Gabor, Attila  |d 910000  |d 912900  |e 910000PG1226773125  |e 912900PG1226773125  |k 0/910000/  |k 1/910000/912900/  |p 29 
998 |g 1207478083  |a Tanevski, Jovan  |m 1207478083:Tanevski, Jovan  |d 910000  |d 912900  |e 910000PT1207478083  |e 912900PT1207478083  |k 0/910000/  |k 1/910000/912900/  |p 1  |x j 
999 |a KXP-PPN1750041030  |e 3879772746 
BIB |a Y 
SER |a journal 
JSO |a {"origin":[{"dateIssuedDisp":"24 September, 2020","dateIssuedKey":"2020"}],"title":[{"title_sort":"Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data","title":"Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data"}],"person":[{"family":"Tanevski","role":"aut","display":"Tanevski, Jovan","given":"Jovan"},{"given":"Thin","display":"Nguyen, Thin","role":"aut","family":"Nguyen"},{"given":"Buu","family":"Truong","role":"aut","display":"Truong, Buu"},{"given":"Nikos","role":"aut","display":"Karaiskos, Nikos","family":"Karaiskos"},{"display":"Ahsen, Mehmet Eren","role":"aut","family":"Ahsen","given":"Mehmet Eren"},{"family":"Zhang","role":"aut","display":"Zhang, Xinyu","given":"Xinyu"},{"given":"Chang","family":"Shu","display":"Shu, Chang","role":"aut"},{"role":"aut","display":"Xu, Ke","family":"Xu","given":"Ke"},{"display":"Liang, Xiaoyu","role":"aut","family":"Liang","given":"Xiaoyu"},{"family":"Hu","display":"Hu, Ying","role":"aut","given":"Ying"},{"given":"Hoang VV","family":"Pham","display":"Pham, Hoang VV","role":"aut"},{"family":"Xiaomei","display":"Xiaomei, Li","role":"aut","given":"Li"},{"display":"Le, Thuc D.","role":"aut","family":"Le","given":"Thuc D."},{"given":"Adi L.","family":"Tarca","display":"Tarca, Adi L.","role":"aut"},{"given":"Gaurav","display":"Bhatti, Gaurav","role":"aut","family":"Bhatti"},{"family":"Romero","role":"aut","display":"Romero, Roberto","given":"Roberto"},{"given":"Nestoras","family":"Karathanasis","display":"Karathanasis, Nestoras","role":"aut"},{"given":"Phillipe","display":"Loher, Phillipe","role":"aut","family":"Loher"},{"given":"Yang","role":"aut","display":"Chen, Yang","family":"Chen"},{"family":"Ouyang","display":"Ouyang, Zhengqing","role":"aut","given":"Zhengqing"},{"family":"Mao","display":"Mao, Disheng","role":"aut","given":"Disheng"},{"display":"Zhang, Yuping","role":"aut","family":"Zhang","given":"Yuping"},{"given":"Maryam","role":"aut","display":"Zand, Maryam","family":"Zand"},{"family":"Ruan","role":"aut","display":"Ruan, Jianhua","given":"Jianhua"},{"display":"Hafemeister, Christoph","role":"aut","family":"Hafemeister","given":"Christoph"},{"family":"Qiu","display":"Qiu, Peng","role":"aut","given":"Peng"},{"given":"Duc","role":"aut","display":"Tran, Duc","family":"Tran"},{"given":"Tin","family":"Nguyen","role":"aut","display":"Nguyen, Tin"},{"display":"Gabor, Attila","role":"aut","family":"Gabor","given":"Attila"},{"role":"aut","display":"Yu, Thomas","family":"Yu","given":"Thomas"},{"given":"Justin","role":"aut","display":"Guinney, Justin","family":"Guinney"},{"display":"Glaab, Enrico","role":"aut","family":"Glaab","given":"Enrico"},{"role":"aut","display":"Krause, Roland","family":"Krause","given":"Roland"},{"family":"Banda","role":"aut","display":"Banda, Peter","given":"Peter"},{"given":"Dream Sctc","display":"Consortium, Dream Sctc","role":"aut","family":"Consortium"},{"family":"Stolovitzky","role":"aut","display":"Stolovitzky, Gustavo","given":"Gustavo"},{"given":"Nikolaus","role":"aut","display":"Rajewsky, Nikolaus","family":"Rajewsky"},{"display":"Sáez Rodríguez, Julio","role":"aut","family":"Sáez Rodríguez","given":"Julio"},{"display":"Meyer, Pablo","role":"aut","family":"Meyer","given":"Pablo"}],"language":["eng"],"physDesc":[{"extent":"13 S."}],"recId":"1750041030","id":{"eki":["1750041030"],"doi":["10.26508/lsa.202000867"]},"name":{"displayForm":["Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang VV Pham, Li Xiaomei, Thuc D. Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Dream Sctc Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer"]},"type":{"bibl":"article-journal","media":"Online-Ressource"},"note":["Gesehen am 01.03.2020"],"relHost":[{"title":[{"title_sort":"Life science alliance","title":"Life science alliance"}],"type":{"media":"Online-Ressource","bibl":"periodical"},"origin":[{"dateIssuedDisp":"[2018]-","publisherPlace":"Heidelberg","publisher":"EMBO Press"}],"pubHistory":["Volume 1, no. 1 (January 2018)-"],"id":{"eki":["1040376843"],"zdb":["2948687-7"],"issn":["2575-1077"]},"recId":"1040376843","disp":"Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics dataLife science alliance","part":{"extent":"13","text":"3(2020,11) Artikel-Nummer 202000867, 13 Seiten","year":"2020","volume":"3","pages":"1-13","issue":"11"},"physDesc":[{"extent":"Online-Ressource"}],"language":["eng"]}]} 
SRT |a TANEVSKIJOGENESELECT2420 

Similar Items