Changes between Version 60 and Version 61 of CapturingGeneExpression


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Timestamp:
Aug 19, 2014, 11:46:54 AM (7 years ago)
Author:
al637
Comment:

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  • CapturingGeneExpression

    v60 v61  
    33= Qualitative Data =
    44
     5
     6These annotations reflect how the amount of transcript/protein level changes in different conditions or at different phases in WT cells.
     7
    58 * Each annotation must consist of these 4 bits of data:
    69  * '''Expression type''' Allowed types: RNA level, protein level, transcription, RNA degradation, translation, protein degradation
     10   * A northern blot (for instance) can only tell you if there is RNA there, and if the amount changes during different conditions. Other assays may tell you specifically if it is transcription or degradation that is affected (for instance, the amount of RNA could increase due to increased transcription or decreased degradation).
    711  * '''Relation''' during(GO biological process ID) or in_presence_of(ChEBI ID), occurs_in(cell type)
     12   * Unstressed conditions include during "vegetative growth of single-celled organism" (=whole cell extract) or "mitotic/meiotic cell cycle" (= they looked at different phases))
     13   * Unstressed conditions include growth on YE and MM unless there is a known difference between the two (in which case EMM might eg be a starvation condition
    814  * '''Level''' allowed qualifiers: present, absent, unchanged, increased, decreased, constant, fluctuates
    915  * '''Evidence''' ECO:xxxxxxx
    10  
    11  * A northern blot (for instance) can only tell you if there is RNA there, and if the amount changes during different conditions. Other assays may tell you specifically if it is transcription or degradation that is affected (for instance, the amount of RNA could increase due to increased transcription or decreased degradation).
    1216
    13  * Unstressed conditions include during "vegetative growth of single-celled organism" (=whole cell extract) or "mitotic/meiotic cell cycle" (= they looked at different phases))
    14  * Unstressed conditions include growth on YE and MM unless there is a known difference between the two
    1517
    1618||'''Examples table'''||