Coexpression is more often due to coregulation than edges.
<p>In the focal GRN from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013387#pcbi.1013387.g006" target="_blank">Fig 6</a>, we show a histogram of coexpression values split by whether pairs of genes share an edge (“A regulates B, or...
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| مؤلفون آخرون: | , , |
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2025
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| _version_ | 1852017061726781440 |
|---|---|
| author | Matthew Aguirre (9558032) |
| author2 | Jeffrey P. Spence (15317543) Guy Sella (230321) Jonathan K. Pritchard (8027465) |
| author2_role | author author author |
| author_facet | Matthew Aguirre (9558032) Jeffrey P. Spence (15317543) Guy Sella (230321) Jonathan K. Pritchard (8027465) |
| author_role | author |
| dc.creator.none.fl_str_mv | Matthew Aguirre (9558032) Jeffrey P. Spence (15317543) Guy Sella (230321) Jonathan K. Pritchard (8027465) |
| dc.date.none.fl_str_mv | 2025-09-02T18:03:02Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1013387.s018 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Coexpression_is_more_often_due_to_coregulation_than_edges_/30037005 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Genetics Molecular Biology Developmental Biology Infectious Diseases Computational Biology Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified world network theory consider future avenues interpret gene coexpression gene knockouts within better understand properties scale perturbation study like hierarchical structure unperturbed cells may gene regulation unperturbed states scale efforts key properties systematically describe remains challenging recent genome recapitulate features perturbation data new approach molecular perturbations modular organization efficient manner deeper analysis |
| dc.title.none.fl_str_mv | Coexpression is more often due to coregulation than edges. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>In the focal GRN from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013387#pcbi.1013387.g006" target="_blank">Fig 6</a>, we show a histogram of coexpression values split by whether pairs of genes share an edge (“A regulates B, or B regulates A”, share a regulator (“A and B are coregulated”), or have another relationship (left panel). Similarly, for perturbation effects, we show the distribution split by whether pairs of genes share an edge (“A regulates B”), a path of distance 2 (“A indirectly regulates B”), or another relationship (right panel). At nearly all levels of coexpression, coregulation is more common than direct regulation. Meanwhile, direct regulation is more common than indirect regulation for the largest perturbation effects—note that the range of KO effects is clipped as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013387#pcbi.1013387.g006" target="_blank">Fig 6</a>.</p> <p>(TIFF)</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_f6abe03b31c13db1dfd4aa855e3a1fb1 |
| identifier_str_mv | 10.1371/journal.pcbi.1013387.s018 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30037005 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Coexpression is more often due to coregulation than edges.Matthew Aguirre (9558032)Jeffrey P. Spence (15317543)Guy Sella (230321)Jonathan K. Pritchard (8027465)GeneticsMolecular BiologyDevelopmental BiologyInfectious DiseasesComputational BiologyBiological Sciences not elsewhere classifiedMathematical Sciences not elsewhere classifiedInformation Systems not elsewhere classifiedworld network theoryconsider future avenuesinterpret gene coexpressiongene knockouts withinbetter understand propertiesscale perturbation studylike hierarchical structureunperturbed cells maygene regulationunperturbed statesscale effortskey propertiessystematically describeremains challengingrecent genomerecapitulate featuresperturbation datanew approachmolecular perturbationsmodular organizationefficient mannerdeeper analysis<p>In the focal GRN from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013387#pcbi.1013387.g006" target="_blank">Fig 6</a>, we show a histogram of coexpression values split by whether pairs of genes share an edge (“A regulates B, or B regulates A”, share a regulator (“A and B are coregulated”), or have another relationship (left panel). Similarly, for perturbation effects, we show the distribution split by whether pairs of genes share an edge (“A regulates B”), a path of distance 2 (“A indirectly regulates B”), or another relationship (right panel). At nearly all levels of coexpression, coregulation is more common than direct regulation. Meanwhile, direct regulation is more common than indirect regulation for the largest perturbation effects—note that the range of KO effects is clipped as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013387#pcbi.1013387.g006" target="_blank">Fig 6</a>.</p> <p>(TIFF)</p>2025-09-02T18:03:02ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1013387.s018https://figshare.com/articles/figure/Coexpression_is_more_often_due_to_coregulation_than_edges_/30037005CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/300370052025-09-02T18:03:02Z |
| spellingShingle | Coexpression is more often due to coregulation than edges. Matthew Aguirre (9558032) Genetics Molecular Biology Developmental Biology Infectious Diseases Computational Biology Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified world network theory consider future avenues interpret gene coexpression gene knockouts within better understand properties scale perturbation study like hierarchical structure unperturbed cells may gene regulation unperturbed states scale efforts key properties systematically describe remains challenging recent genome recapitulate features perturbation data new approach molecular perturbations modular organization efficient manner deeper analysis |
| status_str | publishedVersion |
| title | Coexpression is more often due to coregulation than edges. |
| title_full | Coexpression is more often due to coregulation than edges. |
| title_fullStr | Coexpression is more often due to coregulation than edges. |
| title_full_unstemmed | Coexpression is more often due to coregulation than edges. |
| title_short | Coexpression is more often due to coregulation than edges. |
| title_sort | Coexpression is more often due to coregulation than edges. |
| topic | Genetics Molecular Biology Developmental Biology Infectious Diseases Computational Biology Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified world network theory consider future avenues interpret gene coexpression gene knockouts within better understand properties scale perturbation study like hierarchical structure unperturbed cells may gene regulation unperturbed states scale efforts key properties systematically describe remains challenging recent genome recapitulate features perturbation data new approach molecular perturbations modular organization efficient manner deeper analysis |