Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System Article Swipe
Derek Toms
,
Abdullah Al-Ani
,
Saud Sunba
,
Qing Tong
,
Matthew L. Workentine
,
Mark Ungrin
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.3389/fbioe.2020.00534
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.3389/fbioe.2020.00534
We have developed an accessible software tool (receptoR) to predict potentially active signaling pathways in one or more cell type(s) of interest from publicly available transcriptome data. As proof-of-concept, we applied it to mouse photoreceptors, yielding the previously untested hypothesis that activin signaling pathways are active in these cells. Expression of the type 2 activin receptor (Acvr2a) was experimentally confirmed by both RT-qPCR and immunochemistry, and activation of this signaling pathway with recombinant activin A significantly enhanced the survival of magnetically sorted photoreceptors in culture. Taken together, we demonstrate that our approach can be easily used to mine publicly available transcriptome data and generate hypotheses around receptor expression that can be used to identify novel signaling pathways in specific cell types of interest. We anticipate that receptoR (available at https://www.ucalgary.ca/ungrinlab/receptoR) will enable more efficient use of limited research resources.
Related Topics
Concepts
Biology
Signal transduction
Computational biology
Transcriptome
Receptor
Activin receptor
ACVR2B
Cell biology
Cell type
Immunochemistry
Cell culture
Cell fate determination
Cell
Bioinformatics
Gene expression
Genetics
Gene
TGF beta signaling pathway
Transcription factor
Antibody
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fbioe.2020.00534
- OA Status
- gold
- Cited By
- 1
- References
- 126
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3034015444
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3034015444Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fbioe.2020.00534Digital Object Identifier
- Title
-
Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture SystemWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-06-04Full publication date if available
- Authors
-
Derek Toms, Abdullah Al-Ani, Saud Sunba, Qing Tong, Matthew L. Workentine, Mark UngrinList of authors in order
- Landing page
-
https://doi.org/10.3389/fbioe.2020.00534Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.3389/fbioe.2020.00534Direct OA link when available
- Concepts
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Biology, Signal transduction, Computational biology, Transcriptome, Receptor, Activin receptor, ACVR2B, Cell biology, Cell type, Immunochemistry, Cell culture, Cell fate determination, Cell, Bioinformatics, Gene expression, Genetics, Gene, TGF beta signaling pathway, Transcription factor, AntibodyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
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2021: 1Per-year citation counts (last 5 years)
- References (count)
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126Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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