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GEsture: an online hand-drawing tool for gene expression pattern search

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar...

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Detalles Bibliográficos
Autores principales: Wang, Chunyan, Xu, Yiqing, Wang, Xuelin, Zhang, Li, Wei, Suyun, Ye, Qiaolin, Zhu, Youxiang, Yin, Hengfu, Nainwal, Manoj, Tanon-Reyes, Luis, Cheng, Feng, Yin, Tongming, Ye, Ning
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015481/
https://www.ncbi.nlm.nih.gov/pubmed/29942676
http://dx.doi.org/10.7717/peerj.4927
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author Wang, Chunyan
Xu, Yiqing
Wang, Xuelin
Zhang, Li
Wei, Suyun
Ye, Qiaolin
Zhu, Youxiang
Yin, Hengfu
Nainwal, Manoj
Tanon-Reyes, Luis
Cheng, Feng
Yin, Tongming
Ye, Ning
author_facet Wang, Chunyan
Xu, Yiqing
Wang, Xuelin
Zhang, Li
Wei, Suyun
Ye, Qiaolin
Zhu, Youxiang
Yin, Hengfu
Nainwal, Manoj
Tanon-Reyes, Luis
Cheng, Feng
Yin, Tongming
Ye, Ning
author_sort Wang, Chunyan
collection PubMed
description Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.
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spelling pubmed-60154812018-06-25 GEsture: an online hand-drawing tool for gene expression pattern search Wang, Chunyan Xu, Yiqing Wang, Xuelin Zhang, Li Wei, Suyun Ye, Qiaolin Zhu, Youxiang Yin, Hengfu Nainwal, Manoj Tanon-Reyes, Luis Cheng, Feng Yin, Tongming Ye, Ning PeerJ Bioinformatics Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes. PeerJ Inc. 2018-06-20 /pmc/articles/PMC6015481/ /pubmed/29942676 http://dx.doi.org/10.7717/peerj.4927 Text en ©2018 Wang et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Wang, Chunyan
Xu, Yiqing
Wang, Xuelin
Zhang, Li
Wei, Suyun
Ye, Qiaolin
Zhu, Youxiang
Yin, Hengfu
Nainwal, Manoj
Tanon-Reyes, Luis
Cheng, Feng
Yin, Tongming
Ye, Ning
GEsture: an online hand-drawing tool for gene expression pattern search
title GEsture: an online hand-drawing tool for gene expression pattern search
title_full GEsture: an online hand-drawing tool for gene expression pattern search
title_fullStr GEsture: an online hand-drawing tool for gene expression pattern search
title_full_unstemmed GEsture: an online hand-drawing tool for gene expression pattern search
title_short GEsture: an online hand-drawing tool for gene expression pattern search
title_sort gesture: an online hand-drawing tool for gene expression pattern search
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015481/
https://www.ncbi.nlm.nih.gov/pubmed/29942676
http://dx.doi.org/10.7717/peerj.4927
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