A capsule network-based method for identifying transcription factors Article Swipe
Peijie Zheng
,
Yue Qi
,
Xueyong Li
,
Yuewu Liu
,
Yuhua Yao
,
Guohua Huang
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2022.1048478
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2022.1048478
Transcription factors (TFs) are typical regulators for gene expression and play versatile roles in cellular processes. Since it is time-consuming, costly, and labor-intensive to detect it by using physical methods, it is desired to develop a computational method to detect TFs. Here, we presented a capsule network-based method for identifying TFs. This method is an end-to-end deep learning method, consisting mainly of an embedding layer, bidirectional long short-term memory (LSTM) layer, capsule network layer, and three fully connected layers. The presented method obtained an accuracy of 0.8820, being superior to the state-of-the-art methods. These empirical experiments showed that the inclusion of the capsule network promoted great performances and that the capsule network-based representation was superior to the property-based representation for distinguishing between TFs and non-TFs. We also implemented the presented method into a user-friendly web server, which is freely available at http://www.biolscience.cn/Capsule_TF/ for all scientific researchers.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fmicb.2022.1048478
- https://www.frontiersin.org/articles/10.3389/fmicb.2022.1048478/pdf
- OA Status
- gold
- Cited By
- 1
- References
- 51
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4311706593
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Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4311706593Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3389/fmicb.2022.1048478Digital Object Identifier
- Title
-
A capsule network-based method for identifying transcription factorsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-12-06Full publication date if available
- Authors
-
Peijie Zheng, Yue Qi, Xueyong Li, Yuewu Liu, Yuhua Yao, Guohua HuangList of authors in order
- Landing page
-
https://doi.org/10.3389/fmicb.2022.1048478Publisher landing page
- PDF URL
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https://www.frontiersin.org/articles/10.3389/fmicb.2022.1048478/pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.frontiersin.org/articles/10.3389/fmicb.2022.1048478/pdfDirect OA link when available
- Concepts
-
Computer science, Capsule, Embedding, Representation (politics), Transcription factor, Artificial intelligence, Data mining, Computational biology, Biology, Gene, Politics, Biochemistry, Political science, Law, BotanyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
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51Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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