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Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Authors :
Wang, Zichen
Monteiro, Caroline D.
Jagodnik, Kathleen M.
Fernandez, Nicolas F.
Gundersen, Gregory W.
Rouillard, Andrew D.
Jenkins, Sherry L.
Feldmann, Axel S.
Hu, Kevin S.
McDermott, Michael G.
Duan, Qiaonan
Clark, Neil R.
Jones, Matthew R.
Kou, Yan
Goff, Troy
Woodland, Holly
Amaral, Fabio M R
Szeto, Gregory L.
Fuchs, Oliver
Schüssler-Fiorenza Rose, Sophia M.
Sharma, Shvetank
Schwartz, Uwe
Bausela, Xabier Bengoetxea
Szymkiewicz, Maciej
Maroulis, Vasileios
Salykin, Anton
Barra, Carolina M.
Kruth, Candice D.
Bongio, Nicholas J.
Mathur, Vaibhav
Todoric, Radmila D.
Rubin, Udi E.
Malatras, Apostolos
Fulp, Carl T.
Galindo, John A.
Motiejunaite, Ruta
Jüschke, Christoph
Dishuck, Philip C.
Lahl, Katharina
Jafari, Mohieddin
Aibar, Sara
Zaravinos, Apostolos
Steenhuizen, Linda H.
Allison, Lindsey R.
Gamallo, Pablo
De Andres Segura, Fernando
Dae Devlin, Tyler
Pérez-García, Vicente
Ma'ayan, Avi
Wang, Zichen
Monteiro, Caroline D.
Jagodnik, Kathleen M.
Fernandez, Nicolas F.
Gundersen, Gregory W.
Rouillard, Andrew D.
Jenkins, Sherry L.
Feldmann, Axel S.
Hu, Kevin S.
McDermott, Michael G.
Duan, Qiaonan
Clark, Neil R.
Jones, Matthew R.
Kou, Yan
Goff, Troy
Woodland, Holly
Amaral, Fabio M R
Szeto, Gregory L.
Fuchs, Oliver
Schüssler-Fiorenza Rose, Sophia M.
Sharma, Shvetank
Schwartz, Uwe
Bausela, Xabier Bengoetxea
Szymkiewicz, Maciej
Maroulis, Vasileios
Salykin, Anton
Barra, Carolina M.
Kruth, Candice D.
Bongio, Nicholas J.
Mathur, Vaibhav
Todoric, Radmila D.
Rubin, Udi E.
Malatras, Apostolos
Fulp, Carl T.
Galindo, John A.
Motiejunaite, Ruta
Jüschke, Christoph
Dishuck, Philip C.
Lahl, Katharina
Jafari, Mohieddin
Aibar, Sara
Zaravinos, Apostolos
Steenhuizen, Linda H.
Allison, Lindsey R.
Gamallo, Pablo
De Andres Segura, Fernando
Dae Devlin, Tyler
Pérez-García, Vicente
Ma'ayan, Avi
Source :
Wang , Z , Monteiro , C D , Jagodnik , K M , Fernandez , N F , Gundersen , G W , Rouillard , A D , Jenkins , S L , Feldmann , A S , Hu , K S , McDermott , M G , Duan , Q , Clark , N R , Jones , M R , Kou , Y , Goff , T , Woodland , H , Amaral , F M R , Szeto , G L , Fuchs , O , Schüssler-Fiorenza Rose , S M , Sharma , S , Schwartz , U , Bausela , X B , Szymkiewicz , M , Maroulis , V , Salykin , A , Barra , C M , Kruth , C D , Bongio , N J , Mathur , V , Todoric , R D , Rubin , U E , Malatras , A , Fulp , C T , Galindo , J A , Motiejunaite , R , Jüschke , C , Dishuck , P C , Lahl , K , Jafari , M , Aibar , S , Zaravinos , A , Steenhuizen , L H , Allison , L R , Gamallo , P , De Andres Segura , F , Dae Devlin , T , Pérez-García , V & Ma'ayan , A 2016 , ' Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd ' , Nature Communications , vol. 7 , 12846 .
Publication Year :
2016

Abstract

Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.

Details

Database :
OAIster
Journal :
Wang , Z , Monteiro , C D , Jagodnik , K M , Fernandez , N F , Gundersen , G W , Rouillard , A D , Jenkins , S L , Feldmann , A S , Hu , K S , McDermott , M G , Duan , Q , Clark , N R , Jones , M R , Kou , Y , Goff , T , Woodland , H , Amaral , F M R , Szeto , G L , Fuchs , O , Schüssler-Fiorenza Rose , S M , Sharma , S , Schwartz , U , Bausela , X B , Szymkiewicz , M , Maroulis , V , Salykin , A , Barra , C M , Kruth , C D , Bongio , N J , Mathur , V , Todoric , R D , Rubin , U E , Malatras , A , Fulp , C T , Galindo , J A , Motiejunaite , R , Jüschke , C , Dishuck , P C , Lahl , K , Jafari , M , Aibar , S , Zaravinos , A , Steenhuizen , L H , Allison , L R , Gamallo , P , De Andres Segura , F , Dae Devlin , T , Pérez-García , V & Ma'ayan , A 2016 , ' Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd ' , Nature Communications , vol. 7 , 12846 .
Notes :
application/pdf, English
Publication Type :
Electronic Resource
Accession number :
edsoai.ocn961295202
Document Type :
Electronic Resource