Investigation Title CEA_SGF:E00013#yap1_HU_response
Comment[Submitted Name] CEA_SGF:E00013#yap1_HU_response
Experimental Design
Experimental Design Term Source REF
Comment[SecondaryAccession] GSE1941
Comment[ArrayExpressReleaseDate] 2005-11-30
Comment[AEMIAMESCORE] 1
Comment[ArrayExpressAccession] E-GEOD-1941
Comment[MAGETAB TimeStamp_Version] 2010-10-14 19:52:09 Last Changed Rev: 14677
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Person Last Name Dubacq
Person First Name Caroline
Person Mid Initials
Person Email cdubacq@biologie.ens.fr
Person Phone 33-1 44 32 39 30
Person Fax 33-1 44 32 27 27
Person Address Biologie, Ecole Normale Supérieure, 45 rue d'Ulm, Paris, France
Person Affiliation Ecole Normale Supérieure
Person Roles submitter
Person Roles Term Source REF The MGED Ontology
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date 2005-11-30
PubMed ID
Publication DOI
Publication Author List
Publication Title
Publication Status
Publication Status Term Source REF
Experiment Description Analysis of the response to hydroxyurea in a yeast yap1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours.
Protocol Name P-GSE1941-1
Protocol Type bioassay_data_transformation
Protocol Description ID_REF =
VALUE = log2 ratio of the median intensities of each feature for each wavelength, with the median background not subtracted.
DIA = the diameter in µm of the feature-indicator.
F635_Median = median feature pixel intensity at wavelength #1 (635 nm).
F635_Mean = mean feature pixel intensity at wavelength #1 (635 nm).
F635_SD = the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
B635_Median = the median feature background intensity at wavelength #1 (635 nm).
B635_Mean = the mean feature background intensity at wavelength #1 (635 nm).
B635_SD = the standard deviation of the feature background intensity at wavelength #1 (635 nm).
%_>_B635+1SD = the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
%_>_B635+2SD = the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635_%_Sat = the percentage of feature pixels at wavelength #1 that are saturated.
F532_Median = median feature pixel intensity at wavelength #2 (532 nm).
F532_Mean = mean feature pixel intensity at wavelength #2 (532 nm).
F532_SD = the standard deviation of the feature intensity at wavelength #2 (532 nm).
B532_Median = the median feature background intensity at wavelength #2 (532 nm).
B532_Mean = the mean feature background intensity at wavelength #2 (532 nm).
B532_SD = the standard deviation of the feature background intensity at wavelength #2 (532 nm).
%_>_B532+1SD = the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
%_>_B532+2SD = the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532_%_Sat = the percentage of feature pixels at wavelength #2 that are saturated.
Ratio_of_Medians_(635/532) = the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio_of_Means_(635/532) = the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median_of_Ratios_(635/532) = the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean_of_Ratios_(635/532) = the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios_SD_(635/532) = the geometric standard deviation of the pixel intensity ratios.
Rgn_Ratio_(635/532) = the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn_R²_(635/532) = the coefficient of determination for the current regression value.
Flags = the type of flag associated with a feature.
Protocol Parameters
Protocol Hardware
Protocol Software
Protocol Contact
Protocol Term Source REF The MGED Ontology
SDRF File E-GEOD-1941.sdrf.txt
Term Source Name EFO The MGED Ontology ArrayExpress The MGED Ontology
Term Source File http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version