Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development
Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-...
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| Veröffentlicht in: | PloS one 2013-04, Vol.8 (4), p.e60494-e60494 |
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| creator | Busch, Hauke Boerries, Melanie Bao, Jie Hanke, Sebastian T Hiss, Manuel Tiko, Theodhor Rensing, Stefan A |
| description | Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems. |
| doi_str_mv | 10.1371/journal.pone.0060494 |
| format | Article |
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Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0060494</identifier><identifier>PMID: 23637751</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Basic Helix-Loop-Helix Transcription Factors - physiology ; Biology ; Bryopsida - genetics ; Bryopsida - growth & development ; Cancer ; Cell Transdifferentiation - genetics ; Consortia ; Correlation analysis ; Decision analysis ; Decisions ; DNA binding proteins ; Gene expression ; Gene Expression Profiling - methods ; Gene Expression Regulation, Plant - physiology ; Gene Ontology ; Genetic research ; Genomes ; Kinetics ; Medical research ; Physcomitrella patens ; Plant Leaves - cytology ; Pluripotency ; Proteins ; Regulators ; Signaling ; Statistical analysis ; Stem cell transplantation ; Stem cells ; Stem Cells - physiology ; Stress, Physiological - genetics ; Studies ; Systems analysis ; Systems Theory ; Tissue Array Analysis ; Trajectory analysis ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcriptome - physiology</subject><ispartof>PloS one, 2013-04, Vol.8 (4), p.e60494-e60494</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Busch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Busch et al 2013 Busch et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-808ba35807a0e85bfd53c3c4bd287b0e28bd7a971d75d357ac777b76f8bbe8d63</citedby><cites>FETCH-LOGICAL-c758t-808ba35807a0e85bfd53c3c4bd287b0e28bd7a971d75d357ac777b76f8bbe8d63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630159/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630159/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23637751$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Benos, Panayiotis V.</contributor><creatorcontrib>Busch, Hauke</creatorcontrib><creatorcontrib>Boerries, Melanie</creatorcontrib><creatorcontrib>Bao, Jie</creatorcontrib><creatorcontrib>Hanke, Sebastian T</creatorcontrib><creatorcontrib>Hiss, Manuel</creatorcontrib><creatorcontrib>Tiko, Theodhor</creatorcontrib><creatorcontrib>Rensing, Stefan A</creatorcontrib><title>Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.</description><subject>Basic Helix-Loop-Helix Transcription Factors - physiology</subject><subject>Biology</subject><subject>Bryopsida - genetics</subject><subject>Bryopsida - growth & development</subject><subject>Cancer</subject><subject>Cell Transdifferentiation - genetics</subject><subject>Consortia</subject><subject>Correlation analysis</subject><subject>Decision analysis</subject><subject>Decisions</subject><subject>DNA binding proteins</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation, Plant - physiology</subject><subject>Gene Ontology</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Kinetics</subject><subject>Medical research</subject><subject>Physcomitrella patens</subject><subject>Plant Leaves - cytology</subject><subject>Pluripotency</subject><subject>Proteins</subject><subject>Regulators</subject><subject>Signaling</subject><subject>Statistical analysis</subject><subject>Stem cell transplantation</subject><subject>Stem cells</subject><subject>Stem Cells - 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| subjects | Basic Helix-Loop-Helix Transcription Factors - physiology Biology Bryopsida - genetics Bryopsida - growth & development Cancer Cell Transdifferentiation - genetics Consortia Correlation analysis Decision analysis Decisions DNA binding proteins Gene expression Gene Expression Profiling - methods Gene Expression Regulation, Plant - physiology Gene Ontology Genetic research Genomes Kinetics Medical research Physcomitrella patens Plant Leaves - cytology Pluripotency Proteins Regulators Signaling Statistical analysis Stem cell transplantation Stem cells Stem Cells - physiology Stress, Physiological - genetics Studies Systems analysis Systems Theory Tissue Array Analysis Trajectory analysis Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcriptome - physiology |
| title | Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development |
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