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

Zichen Wang; Caroline D. Monteiro; Kathleen M. Jagodnik; Nicolas F. Fernandez; Gregory W. Gundersen; Andrew D. Rouillard; Sherry L. Jenkins; Axel S. Feldmann; Kevin S. Hu; Michael G. McDermott; Qiaonan Duan; Neil R. Clark; Matthew R. Jones; Yan Kou; Troy Goff; Holly Woodland; Fabio M R Amaral; Gregory L. Szeto; Oliver Fuchs; Sophia M. Schüssler-Fiorenza Rose; Shvetank Sharma; Uwe Schwartz; Xabier Bengoetxea Bausela; Maciej Szymkiewicz; Vasileios Maroulis; Anton Salykin; Carolina M. Barra; Candice D. Kruth; Nicholas J. Bongio; Vaibhav Mathur; Radmila D. Todoric; Udi E. Rubin; Apostolos Malatras; Carl T. Fulp; John A. Galindo; Ruta Motiejunaite; Christoph Jüschke; Philip C. Dishuck; Katharina Lahl; Mohieddin Jafari; Sara Aibar; Apostolos Zaravinos; Linda H. Steenhuizen; Lindsey R. Allison; Pablo Gamallo; Fernando De Andres Segura; Tyler Dae Devlin; Vicente Pérez-García; Avi Ma'ayan

doi:10.1038/ncomms12846

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

Zichen Wang, Caroline D. Monteiro, Kathleen M. Jagodnik, Nicolas F. Fernandez, Gregory W. Gundersen, Andrew D. Rouillard, Sherry L. Jenkins, Axel S. Feldmann, Kevin S. Hu, Michael G. McDermott, Qiaonan Duan, Neil R. Clark, Matthew R. Jones, Yan Kou, Troy Goff, Holly Woodland, Fabio M R Amaral, Gregory L. Szeto, Oliver Fuchs, Sophia M. Schüssler-Fiorenza RoseShvetank Sharma, Uwe Schwartz, Xabier Bengoetxea Bausela, Maciej Szymkiewicz, Vasileios Maroulis, Anton Salykin, Carolina M. Barra, Candice D. Kruth, Nicholas J. Bongio, Vaibhav Mathur, Radmila D. Todoric, Udi E. Rubin, Apostolos Malatras, Carl T. Fulp, John A. Galindo, Ruta Motiejunaite, Christoph Jüschke, Philip C. Dishuck, Katharina Lahl, Mohieddin Jafari, Sara Aibar, Apostolos Zaravinos, Linda H. Steenhuizen, Lindsey R. Allison, Pablo Gamallo, Fernando De Andres Segura, Tyler Dae Devlin, Vicente Pérez-García, Avi Ma'ayan

Research output: Contribution to journal › Journal article › Research › peer-review

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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.

Original language	English
Article number	12846
Journal	Nature Communications
Volume	7
Number of pages	11
ISSN	2041-1723
DOIs	https://doi.org/10.1038/ncomms12846
Publication status	Published - 2016

Keywords

Chemistry (all)
Biochemistry, Genetics and Molecular Biology (all)
Physics and Astronomy (all)

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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., ... Ma'ayan, A. (2016). Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nature Communications, 7, [12846]. https://doi.org/10.1038/ncomms12846

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. / Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. In: Nature Communications. 2016 ; Vol. 7.

@article{d703c2248cf543848563abe57eb4ddb3,

title = "Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd",

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.",

keywords = "Chemistry (all), Biochemistry, Genetics and Molecular Biology (all), Physics and Astronomy (all)",

author = "Zichen Wang and Monteiro, {Caroline D.} and Jagodnik, {Kathleen M.} and Fernandez, {Nicolas F.} and Gundersen, {Gregory W.} and Rouillard, {Andrew D.} and Jenkins, {Sherry L.} and Feldmann, {Axel S.} and Hu, {Kevin S.} and McDermott, {Michael G.} and Qiaonan Duan and Clark, {Neil R.} and Jones, {Matthew R.} and Yan Kou and Troy Goff and Holly Woodland and Amaral, {Fabio M R} and Szeto, {Gregory L.} and Oliver Fuchs and {Sch{\"u}ssler-Fiorenza Rose}, {Sophia M.} and Shvetank Sharma and Uwe Schwartz and Bausela, {Xabier Bengoetxea} and Maciej Szymkiewicz and Vasileios Maroulis and Anton Salykin and Barra, {Carolina M.} and Kruth, {Candice D.} and Bongio, {Nicholas J.} and Vaibhav Mathur and Todoric, {Radmila D.} and Rubin, {Udi E.} and Apostolos Malatras and Fulp, {Carl T.} and Galindo, {John A.} and Ruta Motiejunaite and Christoph J{\"u}schke and Dishuck, {Philip C.} and Katharina Lahl and Mohieddin Jafari and Sara Aibar and Apostolos Zaravinos and Steenhuizen, {Linda H.} and Allison, {Lindsey R.} and Pablo Gamallo and {De Andres Segura}, Fernando and {Dae Devlin}, Tyler and Vicente P{\'e}rez-Garc{\'i}a and Avi Ma'ayan",

year = "2016",

doi = "10.1038/ncomms12846",

language = "English",

volume = "7",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

Wang, Z, Monteiro, CD, Jagodnik, KM, Fernandez, NF, Gundersen, GW, Rouillard, AD, Jenkins, SL, Feldmann, AS, Hu, KS, McDermott, MG, Duan, Q, Clark, NR, Jones, MR, Kou, Y, Goff, T, Woodland, H, Amaral, FMR, Szeto, GL, Fuchs, O, Schüssler-Fiorenza Rose, SM, Sharma, S, Schwartz, U, Bausela, XB, Szymkiewicz, M, Maroulis, V, Salykin, A, Barra, CM, Kruth, CD, Bongio, NJ, Mathur, V, Todoric, RD, Rubin, UE, Malatras, A, Fulp, CT, Galindo, JA, Motiejunaite, R, Jüschke, C, Dishuck, PC, Lahl, K, Jafari, M, Aibar, S, Zaravinos, A, Steenhuizen, LH, Allison, LR, 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. https://doi.org/10.1038/ncomms12846

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

In: Nature Communications, Vol. 7, 12846, 2016.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

AU - Wang, Zichen

AU - Monteiro, Caroline D.

AU - Jagodnik, Kathleen M.

AU - Fernandez, Nicolas F.

AU - Gundersen, Gregory W.

AU - Rouillard, Andrew D.

AU - Jenkins, Sherry L.

AU - Feldmann, Axel S.

AU - Hu, Kevin S.

AU - McDermott, Michael G.

AU - Duan, Qiaonan

AU - Clark, Neil R.

AU - Jones, Matthew R.

AU - Kou, Yan

AU - Goff, Troy

AU - Woodland, Holly

AU - Amaral, Fabio M R

AU - Szeto, Gregory L.

AU - Fuchs, Oliver

AU - Schüssler-Fiorenza Rose, Sophia M.

AU - Sharma, Shvetank

AU - Schwartz, Uwe

AU - Bausela, Xabier Bengoetxea

AU - Szymkiewicz, Maciej

AU - Maroulis, Vasileios

AU - Salykin, Anton

AU - Barra, Carolina M.

AU - Kruth, Candice D.

AU - Bongio, Nicholas J.

AU - Mathur, Vaibhav

AU - Todoric, Radmila D.

AU - Rubin, Udi E.

AU - Malatras, Apostolos

AU - Fulp, Carl T.

AU - Galindo, John A.

AU - Motiejunaite, Ruta

AU - Jüschke, Christoph

AU - Dishuck, Philip C.

AU - Lahl, Katharina

AU - Jafari, Mohieddin

AU - Aibar, Sara

AU - Zaravinos, Apostolos

AU - Steenhuizen, Linda H.

AU - Allison, Lindsey R.

AU - Gamallo, Pablo

AU - De Andres Segura, Fernando

AU - Dae Devlin, Tyler

AU - Pérez-García, Vicente

AU - Ma'ayan, Avi

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - Chemistry (all)

KW - Biochemistry, Genetics and Molecular Biology (all)

KW - Physics and Astronomy (all)

U2 - 10.1038/ncomms12846

DO - 10.1038/ncomms12846

M3 - Journal article

C2 - 27667448

VL - 7

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 12846

ER -