Calculated rates of protein synthesis in the light and dark in Ostreococcus tauri Version 2
ExploreSEEK ID: https://fairdomhub.org/data_files/2052?version=2
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Otauri_dark_and_light_protein_synthesis.csv
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Ot gene Idb,Incorporation in the light,Incorporation in the dark OtCpg00590,0.140021082221,0.052222417428 OtCpg00100,0.128812172775,0.0321498691099 Ot18g02040,0.19183563771,0.0117657598471 Ot08g01880,0.283389893543,-0.103481939473 Ot05g03850,0.0903717826501,0.0296472831268 Ot12g01070,0.102764250931,0.0534230879404 Ot03g04370,0.0544992320322,0.113844605688 OtCpg00470,0.154169405578,0.0573880176542 Ot13g00910,0.135677137508,0.0281672560849 Ot01g06200,0.12283790782,0.0761263593993 Ot04g02690,0.186386130608,0.000566031633082 Ot14g01370,0.201346801347,0.0187205387205 OtCpg00250,0.111836952652,0.0477928088288 Ot13g00230,0.185476940705,0.0216270409625 Ot01g03020,0.111359264091,0.0664042633173 Ot10g03300,0.1670850487,0.0328948689627 Ot05g01790,0.130889756208,0.013858249901 Ot16g02550,0.0652613341034,0.0451920300318 Ot10g03520,0.19035385617,0.000563072970738 OtCpg00010,0.182491289199,0.030487804878 Ot10g02850,0.202043345979,0.0152499718289 Ot01g01490,0.205999727462,0.0282855418638 OtCpg00040 ,0.184008609522,0.00532116308269 Ot07g04240,0.167696601216,0.0210056812519 Ot03g00210,0.0613495391879,0.0780492704854 Ot14g00200,0.202693429405,0.00917824669755 Ot12g00400,0.158423657285,-0.0164252967787 Ot04g01880,0.167217881156,0.0373977830274 Ot18g01370 ,0.130240036752,0.00692929060909 Ot02g06800,0.36834863888,0.0630493890521 Ot14g02820,0.0726642590867,0.0936626281454 Ot16g01660,0.167631201464,-0.0152347034674 Ot16g00030,-0.0390650718753,0.175171001134 Ot04g02900,0.104184100418,0.0260529986053 Ot01g04890,0.198834437086,0.0323178807947 Ot02g00850,0.0318870468787,0.0968906163243 Ot18g01390,0.100726367654,0.0979834408493 OtCpg00180,0.121760929666,0.0212501757181 Ot09g04190,0.235565819861,0.0302430440999 OtMtg00170,0.162865830483,-0.029152413531
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Created: 15th Jan 2018 at 21:12
Last updated: 21st Feb 2018 at 11:31
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Version History
Version 2 (latest) Created 21st Feb 2018 at 11:31 by Daniel Seaton
Corrects labelling of columns - the 'light' and 'dark' columns were swapped in the previous version.
Related items
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Institutions: University of Edinburgh, School of Biological Sciences, University of Edinburgh
https://orcid.org/0000-0003-1756-3654
The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
Andrew Millar's research group, University of Edinburgh
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: http://www.amillar.org
Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.
Submitter: Andrew Millar
Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model
Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data
Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
