Temporal clustering analysis of endothelial cell gene expression following exposure to a conventional radiotherapy dose fraction using Gaussian process clustering Article Swipe
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· 2018
· Open Access
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· DOI: https://doi.org/10.1371/journal.pone.0204960
The vascular endothelium is considered as a key cell compartment for the response to ionizing radiation of normal tissues and tumors, and as a promising target to improve the differential effect of radiotherapy in the future. Following radiation exposure, the global endothelial cell response covers a wide range of gene, miRNA, protein and metabolite expression modifications. Changes occur at the transcriptional, translational and post-translational levels and impact cell phenotype as well as the microenvironment by the production and secretion of soluble factors such as reactive oxygen species, chemokines, cytokines and growth factors. These radiation-induced dynamic modifications of molecular networks may control the endothelial cell phenotype and govern recruitment of immune cells, stressing the importance of clearly understanding the mechanisms which underlie these temporal processes. A wide variety of time series data is commonly used in bioinformatics studies, including gene expression, protein concentrations and metabolomics data. The use of clustering of these data is still an unclear problem. Here, we introduce kernels between Gaussian processes modeling time series, and subsequently introduce a spectral clustering algorithm. We apply the methods to the study of human primary endothelial cells (HUVECs) exposed to a radiotherapy dose fraction (2 Gy). Time windows of differential expressions of 301 genes involved in key cellular processes such as angiogenesis, inflammation, apoptosis, immune response and protein kinase were determined from 12 hours to 3 weeks post-irradiation. Then, 43 temporal clusters corresponding to profiles of similar expressions, including 49 genes out of 301 initially measured, were generated according to the proposed method. Forty-seven transcription factors (TFs) responsible for the expression of clusters of genes were predicted from sequence regulatory elements using the MotifMap system. Their temporal profiles of occurrences were established and clustered. Dynamic network interactions and molecular pathways of TFs and differential genes were finally explored, revealing key node genes and putative important cellular processes involved in tissue infiltration by immune cells following exposure to a radiotherapy dose fraction.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pone.0204960
- https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0204960&type=printable
- OA Status
- gold
- Cited By
- 6
- References
- 68
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2895607736
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2895607736Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1371/journal.pone.0204960Digital Object Identifier
- Title
-
Temporal clustering analysis of endothelial cell gene expression following exposure to a conventional radiotherapy dose fraction using Gaussian process clusteringWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2018Year of publication
- Publication date
-
2018-10-03Full publication date if available
- Authors
-
Markus Heinonen, Fabien Milliat, Mohamed Amine Benadjaoud, Agnès François, Valérie Buard, Georges Tarlet, Florence d’Alché–Buc, Olivier GuipaudList of authors in order
- Landing page
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https://doi.org/10.1371/journal.pone.0204960Publisher landing page
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0204960&type=printableDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0204960&type=printableDirect OA link when available
- Concepts
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Angiogenesis, Biology, Gene expression, Chemokine, Computational biology, Bioinformatics, Inflammation, Cell biology, Gene, Cancer research, Immunology, GeneticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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6Total citation count in OpenAlex
- Citations by year (recent)
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2024: 2, 2022: 1, 2021: 2, 2020: 1Per-year citation counts (last 5 years)
- References (count)
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68Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.expression | 54, 259 |
| abstract_inverted_index.importance | 113 |
| abstract_inverted_index.mechanisms | 118 |
| abstract_inverted_index.metabolite | 53 |
| abstract_inverted_index.processes. | 123 |
| abstract_inverted_index.production | 76 |
| abstract_inverted_index.regulatory | 268 |
| abstract_inverted_index.Forty-seven | 252 |
| abstract_inverted_index.chemokines, | 87 |
| abstract_inverted_index.compartment | 9 |
| abstract_inverted_index.endothelial | 41, 102, 184 |
| abstract_inverted_index.endothelium | 2 |
| abstract_inverted_index.established | 280 |
| abstract_inverted_index.expression, | 139 |
| abstract_inverted_index.expressions | 199 |
| abstract_inverted_index.occurrences | 278 |
| abstract_inverted_index.recruitment | 107 |
| abstract_inverted_index.responsible | 256 |
| abstract_inverted_index.differential | 29, 198, 292 |
| abstract_inverted_index.expressions, | 236 |
| abstract_inverted_index.infiltration | 309 |
| abstract_inverted_index.interactions | 285 |
| abstract_inverted_index.metabolomics | 143 |
| abstract_inverted_index.radiotherapy | 32, 190, 317 |
| abstract_inverted_index.subsequently | 168 |
| abstract_inverted_index.angiogenesis, | 210 |
| abstract_inverted_index.corresponding | 231 |
| abstract_inverted_index.inflammation, | 211 |
| abstract_inverted_index.modifications | 95 |
| abstract_inverted_index.transcription | 253 |
| abstract_inverted_index.translational | 61 |
| abstract_inverted_index.understanding | 116 |
| abstract_inverted_index.bioinformatics | 135 |
| abstract_inverted_index.concentrations | 141 |
| abstract_inverted_index.modifications. | 55 |
| abstract_inverted_index.microenvironment | 73 |
| abstract_inverted_index.transcriptional, | 60 |
| abstract_inverted_index.post-irradiation. | 226 |
| abstract_inverted_index.radiation-induced | 93 |
| abstract_inverted_index.post-translational | 63 |
| cited_by_percentile_year.max | 96 |
| cited_by_percentile_year.min | 89 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 8 |
| citation_normalized_percentile.value | 0.58154721 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |