Sce stressed expression
h qin
2016 March 29
See http://www.ncbi.nlm.nih.gov/pubmed/19536156
GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array
rm(list=ls())
setwd("~/github/GSE15936_yeast_stress")
library(Biobase)
library(GEOquery)
library(limma)
library(foreach)
library(doMC) gset <- getGEO(filename="GSE15936_series_matrix.txt.gz")## File stored at:## /var/folders/nl/4nhwcdy107z85j39348mvctm0000gp/T//RtmpxcFHA4/GPL2529.softex <- exprs(gset)means = apply(ex, 2, mean)
scale = max(means)
for(i in 1:length(ex[1,])){
ex[,i] = ex[,i] * scale/ means[i]
}
apply( ex, 2, mean) / scale## GSM399864 GSM399865 GSM399866 GSM399867 GSM399868 GSM399869 GSM399870
## 1 1 1 1 1 1 1
## GSM399871 GSM399872 GSM399873 GSM399874 GSM399875 GSM399876 GSM399877
## 1 1 1 1 1 1 1
## GSM399878 GSM399879 GSM399880 GSM399881 GSM399882 GSM399883 GSM399884
## 1 1 1 1 1 1 1
## GSM399885
## 1apply( ex, 2, median) ## GSM399864 GSM399865 GSM399866 GSM399867 GSM399868 GSM399869 GSM399870
## 6.194682 6.192348 6.893271 6.818016 6.982195 6.889762 6.285414
## GSM399871 GSM399872 GSM399873 GSM399874 GSM399875 GSM399876 GSM399877
## 6.523725 6.607421 6.602101 6.401853 6.359068 6.492761 6.245131
## GSM399878 GSM399879 GSM399880 GSM399881 GSM399882 GSM399883 GSM399884
## 6.328471 6.260902 6.589425 6.406905 6.490374 6.209000 6.457136
## GSM399885
## 6.051965boxplot( ex )
What is boxplot? See http://tinyurl.com/zw7bd9jStudy the structure of gset
str(gset)Formal class 'ExpressionSet' [package "Biobase"] with 7 slots
..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots
.. .. ..@ name : chr ""
.. .. ..@ lab : chr ""
.. .. ..@ contact : chr ""
.. .. ..@ title : chr ""
.. .. ..@ abstract : chr ""
.. .. ..@ url : chr ""
.. .. ..@ pubMedIds : chr ""
.. .. ..@ samples : list()
.. .. ..@ hybridizations : list()
.. .. ..@ normControls : list()
.. .. ..@ preprocessing : list()
.. .. ..@ other : list()
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
.. .. .. .. ..@ .Data:List of 2
.. .. .. .. .. ..$ : int [1:3] 1 0 0
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ assayData :<environment: 0x7fe2d794d0b0>
..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 33 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr [1:33] NA NA NA NA ...
.. .. ..@ data :'data.frame': 22 obs. of 33 variables:
.. .. .. ..$ title : Factor w/ 22 levels "Heat shock, t30 min",..: 21 22 1 2 3 4 13 14 15 16 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ geo_accession : Factor w/ 22 levels "GSM399864","GSM399865",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ status : Factor w/ 1 level "Public on Aug 07 2009": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ submission_date : Factor w/ 1 level "May 03 2009": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ last_update_date : Factor w/ 1 level "Aug 07 2009": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ type : Factor w/ 1 level "RNA": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ channel_count : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ source_name_ch1 : Factor w/ 8 levels "H2O2 treated S. cerevisiae cells",..: 8 8 4 4 5 5 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ organism_ch1 : Factor w/ 1 level "Saccharomyces cerevisiae": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ characteristics_ch1 : Factor w/ 1 level "strain: 4741": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ characteristics_ch1.1 : Factor w/ 8 levels "stress: heat stress",..: 8 8 1 1 4 4 7 7 7 7 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ characteristics_ch1.2 : Factor w/ 5 levels "time: 0 min",..: 1 1 3 4 3 4 2 3 4 5 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ treatment_protocol_ch1 : Factor w/ 1 level "At time 0 cells were treated with mild stresses and then transftered to another stress": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ growth_protocol_ch1 : Factor w/ 1 level "Cells were grown in YPD to mid log phase in 30 degrees": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ molecule_ch1 : Factor w/ 1 level "total RNA": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ extract_protocol_ch1 : Factor w/ 1 level "Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ label_ch1 : Factor w/ 1 level "biotin": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ label_protocol_ch1 : Factor w/ 1 level "cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ taxid_ch1 : Factor w/ 1 level "4932": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ hyb_protocol : Factor w/ 1 level "According to standard Affymetrix protocol": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ scan_protocol : Factor w/ 1 level "According to standard Affymetrix protocol": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ description : Factor w/ 21 levels "Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 15min",..: 21 21 13 14 15 16 9 10 11 12 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ data_processing : Factor w/ 1 level "RMA algorithms using bioconductor software implemented in R": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ platform_id : Factor w/ 1 level "GPL2529": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_name : Factor w/ 1 level "Amir,,Mitchell": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_email : Factor w/ 1 level "amir.mitchell@weizmann.ac.il": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_institute : Factor w/ 1 level "Weizmann Inst.": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_address : Factor w/ 1 level "Hertzel": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_city : Factor w/ 1 level "Rehovot": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_zip/postal_code: Factor w/ 1 level "76100": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ contact_country : Factor w/ 1 level "Israel": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ supplementary_file : Factor w/ 22 levels "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399864/GSM399864.CEL.gz",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. .. ..$ data_row_count : Factor w/ 1 level "10928": 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..- attr(*, "names")= chr [1:22] "V2" "V3" "V4" "V5" ...
.. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 16 obs. of 3 variables:
.. .. .. ..$ Column : chr [1:16] "ID" "ORF" "SPOT_ID" "ORGANISM" ...
.. .. .. ..$ Description : Factor w/ 15 levels "","A gene symbol, when one is available (from UniGene).",..: 3 5 1 11 14 12 13 1 6 15 ...
.. .. .. ..$ labelDescription: chr [1:16] NA NA NA NA ...
.. .. ..@ data :'data.frame': 10928 obs. of 16 variables:
.. .. .. ..$ ID : Factor w/ 10929 levels "1769308_at","1769309_at",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. ..$ ORF : Factor w/ 10640 levels "SPAC1039.07c",..: 80 17 40 51 63 67 59 30 12 86 ...
.. .. .. ..$ SPOT_ID : chr [1:10928] NA NA NA NA ...
.. .. .. ..$ ORGANISM : Factor w/ 5 levels "Saccharomyces cerevisiae",..: 1 2 2 1 1 1 1 2 2 1 ...
.. .. .. ..$ Annotation Date : Factor w/ 2 levels "Mar 13, 2009",..: 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. ..$ Representative Public ID : Factor w/ 10845 levels "SPAC1039.07c.S1",..: 80 17 40 51 63 67 59 30 12 86 ...
.. .. .. ..$ Sequence Source : Factor w/ 2 levels "Affymetrix Proprietary Database",..: 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. ..$ Transcript ID(Array Design) : Factor w/ 10715 levels "SPAC1039.07c",..: 80 17 40 51 63 67 59 30 12 86 ...
.. .. .. ..$ Target Description : Factor w/ 10783 levels "S. cerevisiae YBR238C /GEN=PRP5 /DB_XREF=GI:6319715 /SEG=NC_001134:-695064,697259 /DEF=Hypothetical ORF /NOTE=Ybr238cp; go_comp"| __truncated__,..: 35 72 95 6 18 22 14 85 67 41 ...
.. .. .. ..$ Gene Title : Factor w/ 8221 levels "","19S proteasome regulatory subunit Rpn6",..: 48 37 50 1 53 46 68 23 71 26 ...
.. .. .. ..$ Gene Symbol : Factor w/ 9580 levels "","AIF1","AMD1",..: 21 25 74 1 38 41 40 6 64 15 ...
.. .. .. ..$ ENTREZ_GENE_ID : Factor w/ 4929 levels "","2538761","2538786",..: 1 14 8 1 1 1 1 18 32 1 ...
.. .. .. ..$ SGD accession number : Factor w/ 5699 levels "","S000000442",..: 17 1 1 23 7 32 31 1 1 40 ...
.. .. .. ..$ Gene Ontology Biological Process: Factor w/ 6706 levels "","0000001 // mitochondrion inheritance // inferred from mutant phenotype /// 0006200 // ATP catabolic process // inferred from mu"| __truncated__,..: 51 31 79 1 26 73 43 34 1 6 ...
.. .. .. ..$ Gene Ontology Cellular Component: Factor w/ 5130 levels "","0000127 // transcription factor TFIIIC complex // inferred from direct assay /// 0005634 // nucleus // inferred from direct ass"| __truncated__,..: 77 11 28 61 5 61 7 22 81 21 ...
.. .. .. ..$ Gene Ontology Molecular Function: Factor w/ 5276 levels "","0000166 // nucleotide binding // inferred from electronic annotation /// 0000287 // magnesium ion binding // inferred from elec"| __truncated__,..: 31 19 1 1 62 47 13 7 1 17 ...
.. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ annotation : chr "GPL2529"
..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr(0)
.. .. ..@ data :'data.frame': 22 obs. of 0 variables
.. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
.. .. ..@ .Data:List of 4
.. .. .. ..$ : int [1:3] 3 2 0
.. .. .. ..$ : int [1:3] 2 28 0
.. .. .. ..$ : int [1:3] 1 3 0
.. .. .. ..$ : int [1:3] 1 0 0gset@phenoData@data title geo_accession
GSM399864 Untreated, t0_a GSM399864
GSM399865 Untreated, t0_b GSM399865
GSM399866 Heat shock, t30 min GSM399866
GSM399867 Heat shock, t45 min GSM399867
GSM399868 Osmotic stress, t30 min GSM399868
GSM399869 Osmotic stress, t45 min GSM399869
GSM399870 Oxidative stress, t15 min GSM399870
GSM399871 Oxidative stress, t30 min GSM399871
GSM399872 Oxidative stress, t45 min GSM399872
GSM399873 Oxidative stress, t90 min GSM399873
GSM399874 Oxidative stress (after heat shock), t15 min GSM399874
GSM399875 Oxidative stress (after heat shock), t30 min GSM399875
GSM399876 Oxidative stress (after heat shock), t45 min GSM399876
GSM399877 Oxidative stress (after heat shock), t90 min GSM399877
GSM399878 Rich media (after heat shock), t15 min GSM399878
GSM399879 Rich media (after heat shock), t45 min GSM399879
GSM399880 Oxidative stress (after osmotic stress), t15 min GSM399880
GSM399881 Oxidative stress (after osmotic stress), t30 min GSM399881
GSM399882 Oxidative stress (after osmotic stress), t45 min GSM399882
GSM399883 Oxidative stress (after osmotic stress), t90 min GSM399883
GSM399884 Rich media (after osmotic stress), t15 min GSM399884
GSM399885 Rich media (after osmotic stress), t45 min GSM399885
status submission_date last_update_date type
GSM399864 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399865 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399866 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399867 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399868 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399869 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399870 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399871 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399872 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399873 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399874 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399875 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399876 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399877 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399878 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399879 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399880 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399881 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399882 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399883 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399884 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
GSM399885 Public on Aug 07 2009 May 03 2009 Aug 07 2009 RNA
channel_count
GSM399864 1
GSM399865 1
GSM399866 1
GSM399867 1
GSM399868 1
GSM399869 1
GSM399870 1
GSM399871 1
GSM399872 1
GSM399873 1
GSM399874 1
GSM399875 1
GSM399876 1
GSM399877 1
GSM399878 1
GSM399879 1
GSM399880 1
GSM399881 1
GSM399882 1
GSM399883 1
GSM399884 1
GSM399885 1
source_name_ch1
GSM399864 Untreated S. cerevisiae cells
GSM399865 Untreated S. cerevisiae cells
GSM399866 heat treated S. cerevisiae cells
GSM399867 heat treated S. cerevisiae cells
GSM399868 KCl treated S. cerevisiae cells
GSM399869 KCl treated S. cerevisiae cells
GSM399870 H2O2 treated S. cerevisiae cells
GSM399871 H2O2 treated S. cerevisiae cells
GSM399872 H2O2 treated S. cerevisiae cells
GSM399873 H2O2 treated S. cerevisiae cells
GSM399874 H2O2 treated S. cerevisiae cells after priming in heat shock
GSM399875 H2O2 treated S. cerevisiae cells after priming in heat shock
GSM399876 H2O2 treated S. cerevisiae cells after priming in heat shock
GSM399877 H2O2 treated S. cerevisiae cells after priming in heat shock
GSM399878 S. cerevisiae cells transferred to rich media after priming in heat shock
GSM399879 S. cerevisiae cells transferred to rich media after priming in heat shock
GSM399880 H2O2 treated S. cerevisiae cells after priming in osmotic stress
GSM399881 H2O2 treated S. cerevisiae cells after priming in osmotic stress
GSM399882 H2O2 treated S. cerevisiae cells after priming in osmotic stress
GSM399883 H2O2 treated S. cerevisiae cells after priming in osmotic stress
GSM399884 S. cerevisiae cells transferred to rich media after priming in osmotic stress
GSM399885 S. cerevisiae cells transferred to rich media after priming in osmotic stress
organism_ch1 characteristics_ch1
GSM399864 Saccharomyces cerevisiae strain: 4741
GSM399865 Saccharomyces cerevisiae strain: 4741
GSM399866 Saccharomyces cerevisiae strain: 4741
GSM399867 Saccharomyces cerevisiae strain: 4741
GSM399868 Saccharomyces cerevisiae strain: 4741
GSM399869 Saccharomyces cerevisiae strain: 4741
GSM399870 Saccharomyces cerevisiae strain: 4741
GSM399871 Saccharomyces cerevisiae strain: 4741
GSM399872 Saccharomyces cerevisiae strain: 4741
GSM399873 Saccharomyces cerevisiae strain: 4741
GSM399874 Saccharomyces cerevisiae strain: 4741
GSM399875 Saccharomyces cerevisiae strain: 4741
GSM399876 Saccharomyces cerevisiae strain: 4741
GSM399877 Saccharomyces cerevisiae strain: 4741
GSM399878 Saccharomyces cerevisiae strain: 4741
GSM399879 Saccharomyces cerevisiae strain: 4741
GSM399880 Saccharomyces cerevisiae strain: 4741
GSM399881 Saccharomyces cerevisiae strain: 4741
GSM399882 Saccharomyces cerevisiae strain: 4741
GSM399883 Saccharomyces cerevisiae strain: 4741
GSM399884 Saccharomyces cerevisiae strain: 4741
GSM399885 Saccharomyces cerevisiae strain: 4741
characteristics_ch1.1
GSM399864 stress: untreated
GSM399865 stress: untreated
GSM399866 stress: heat stress
GSM399867 stress: heat stress
GSM399868 stress: osmotic stress
GSM399869 stress: osmotic stress
GSM399870 stress: oxidative stress
GSM399871 stress: oxidative stress
GSM399872 stress: oxidative stress
GSM399873 stress: oxidative stress
GSM399874 stress: heat stress followed by oxidative stress
GSM399875 stress: heat stress followed by oxidative stress
GSM399876 stress: heat stress followed by oxidative stress
GSM399877 stress: heat stress followed by oxidative stress
GSM399878 stress: heat stress followed by transfer to rich media
GSM399879 stress: heat stress followed by transfer to rich media
GSM399880 stress: osmotic stress followed by oxidative stress
GSM399881 stress: osmotic stress followed by oxidative stress
GSM399882 stress: osmotic stress followed by oxidative stress
GSM399883 stress: osmotic stress followed by oxidative stress
GSM399884 stress: osmotic stress followed by transfer to rich media
GSM399885 stress: osmotic stress followed by transfer to rich media
characteristics_ch1.2
GSM399864 time: 0 min
GSM399865 time: 0 min
GSM399866 time: 30 min
GSM399867 time: 45 min
GSM399868 time: 30 min
GSM399869 time: 45 min
GSM399870 time: 15 min
GSM399871 time: 30 min
GSM399872 time: 45 min
GSM399873 time: 90 min
GSM399874 time: 15 min
GSM399875 time: 30 min
GSM399876 time: 45 min
GSM399877 time: 90 min
GSM399878 time: 15 min
GSM399879 time: 45 min
GSM399880 time: 15 min
GSM399881 time: 30 min
GSM399882 time: 45 min
GSM399883 time: 90 min
GSM399884 time: 15 min
GSM399885 time: 45 min
treatment_protocol_ch1
GSM399864 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399865 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399866 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399867 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399868 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399869 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399870 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399871 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399872 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399873 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399874 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399875 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399876 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399877 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399878 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399879 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399880 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399881 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399882 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399883 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399884 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399885 At time 0 cells were treated with mild stresses and then transftered to another stress
growth_protocol_ch1
GSM399864 Cells were grown in YPD to mid log phase in 30 degrees
GSM399865 Cells were grown in YPD to mid log phase in 30 degrees
GSM399866 Cells were grown in YPD to mid log phase in 30 degrees
GSM399867 Cells were grown in YPD to mid log phase in 30 degrees
GSM399868 Cells were grown in YPD to mid log phase in 30 degrees
GSM399869 Cells were grown in YPD to mid log phase in 30 degrees
GSM399870 Cells were grown in YPD to mid log phase in 30 degrees
GSM399871 Cells were grown in YPD to mid log phase in 30 degrees
GSM399872 Cells were grown in YPD to mid log phase in 30 degrees
GSM399873 Cells were grown in YPD to mid log phase in 30 degrees
GSM399874 Cells were grown in YPD to mid log phase in 30 degrees
GSM399875 Cells were grown in YPD to mid log phase in 30 degrees
GSM399876 Cells were grown in YPD to mid log phase in 30 degrees
GSM399877 Cells were grown in YPD to mid log phase in 30 degrees
GSM399878 Cells were grown in YPD to mid log phase in 30 degrees
GSM399879 Cells were grown in YPD to mid log phase in 30 degrees
GSM399880 Cells were grown in YPD to mid log phase in 30 degrees
GSM399881 Cells were grown in YPD to mid log phase in 30 degrees
GSM399882 Cells were grown in YPD to mid log phase in 30 degrees
GSM399883 Cells were grown in YPD to mid log phase in 30 degrees
GSM399884 Cells were grown in YPD to mid log phase in 30 degrees
GSM399885 Cells were grown in YPD to mid log phase in 30 degrees
molecule_ch1
GSM399864 total RNA
GSM399865 total RNA
GSM399866 total RNA
GSM399867 total RNA
GSM399868 total RNA
GSM399869 total RNA
GSM399870 total RNA
GSM399871 total RNA
GSM399872 total RNA
GSM399873 total RNA
GSM399874 total RNA
GSM399875 total RNA
GSM399876 total RNA
GSM399877 total RNA
GSM399878 total RNA
GSM399879 total RNA
GSM399880 total RNA
GSM399881 total RNA
GSM399882 total RNA
GSM399883 total RNA
GSM399884 total RNA
GSM399885 total RNA
extract_protocol_ch1
GSM399864 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399865 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399866 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399867 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399868 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399869 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399870 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399871 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399872 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399873 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399874 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399875 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399876 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399877 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399878 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399879 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399880 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399881 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399882 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399883 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399884 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399885 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
label_ch1
GSM399864 biotin
GSM399865 biotin
GSM399866 biotin
GSM399867 biotin
GSM399868 biotin
GSM399869 biotin
GSM399870 biotin
GSM399871 biotin
GSM399872 biotin
GSM399873 biotin
GSM399874 biotin
GSM399875 biotin
GSM399876 biotin
GSM399877 biotin
GSM399878 biotin
GSM399879 biotin
GSM399880 biotin
GSM399881 biotin
GSM399882 biotin
GSM399883 biotin
GSM399884 biotin
GSM399885 biotin
label_protocol_ch1
GSM399864 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399865 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399866 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399867 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399868 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399869 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399870 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399871 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399872 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399873 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399874 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399875 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399876 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399877 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399878 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399879 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399880 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399881 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399882 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399883 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399884 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399885 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
taxid_ch1 hyb_protocol
GSM399864 4932 According to standard Affymetrix protocol
GSM399865 4932 According to standard Affymetrix protocol
GSM399866 4932 According to standard Affymetrix protocol
GSM399867 4932 According to standard Affymetrix protocol
GSM399868 4932 According to standard Affymetrix protocol
GSM399869 4932 According to standard Affymetrix protocol
GSM399870 4932 According to standard Affymetrix protocol
GSM399871 4932 According to standard Affymetrix protocol
GSM399872 4932 According to standard Affymetrix protocol
GSM399873 4932 According to standard Affymetrix protocol
GSM399874 4932 According to standard Affymetrix protocol
GSM399875 4932 According to standard Affymetrix protocol
GSM399876 4932 According to standard Affymetrix protocol
GSM399877 4932 According to standard Affymetrix protocol
GSM399878 4932 According to standard Affymetrix protocol
GSM399879 4932 According to standard Affymetrix protocol
GSM399880 4932 According to standard Affymetrix protocol
GSM399881 4932 According to standard Affymetrix protocol
GSM399882 4932 According to standard Affymetrix protocol
GSM399883 4932 According to standard Affymetrix protocol
GSM399884 4932 According to standard Affymetrix protocol
GSM399885 4932 According to standard Affymetrix protocol
scan_protocol
GSM399864 According to standard Affymetrix protocol
GSM399865 According to standard Affymetrix protocol
GSM399866 According to standard Affymetrix protocol
GSM399867 According to standard Affymetrix protocol
GSM399868 According to standard Affymetrix protocol
GSM399869 According to standard Affymetrix protocol
GSM399870 According to standard Affymetrix protocol
GSM399871 According to standard Affymetrix protocol
GSM399872 According to standard Affymetrix protocol
GSM399873 According to standard Affymetrix protocol
GSM399874 According to standard Affymetrix protocol
GSM399875 According to standard Affymetrix protocol
GSM399876 According to standard Affymetrix protocol
GSM399877 According to standard Affymetrix protocol
GSM399878 According to standard Affymetrix protocol
GSM399879 According to standard Affymetrix protocol
GSM399880 According to standard Affymetrix protocol
GSM399881 According to standard Affymetrix protocol
GSM399882 According to standard Affymetrix protocol
GSM399883 According to standard Affymetrix protocol
GSM399884 According to standard Affymetrix protocol
GSM399885 According to standard Affymetrix protocol
description
GSM399864 Gene expression in Rich media (reference sample)
GSM399865 Gene expression in Rich media (reference sample)
GSM399866 Gene expression in heat shock 40deg, 30min
GSM399867 Gene expression in heat shock 40deg, 45min
GSM399868 Gene expression in KCl 0.8M, 30min
GSM399869 Gene expression in KCl 0.8M, 45min
GSM399870 Gene expression in H2O2 0.66mM, 15min
GSM399871 Gene expression in H2O2 0.66mM, 30min
GSM399872 Gene expression in H2O2 0.66mM, 45min
GSM399873 Gene expression in H2O2 0.66mM, 90min
GSM399874 Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 15min
GSM399875 Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 30min
GSM399876 Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 45min
GSM399877 Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 90min
GSM399878 Gene expression in rich media (after priming 45 min in heat shock), 15min
GSM399879 Gene expression in rich media (after priming 45 min in heat shock), 45min
GSM399880 Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 15min
GSM399881 Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 30min
GSM399882 Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 45min
GSM399883 Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 90min
GSM399884 Gene expression in rich media (after priming 45 min in osmotic stress), 15min
GSM399885 Gene expression in rich media (after priming 45 min in osmotic stress), 45min
data_processing
GSM399864 RMA algorithms using bioconductor software implemented in R
GSM399865 RMA algorithms using bioconductor software implemented in R
GSM399866 RMA algorithms using bioconductor software implemented in R
GSM399867 RMA algorithms using bioconductor software implemented in R
GSM399868 RMA algorithms using bioconductor software implemented in R
GSM399869 RMA algorithms using bioconductor software implemented in R
GSM399870 RMA algorithms using bioconductor software implemented in R
GSM399871 RMA algorithms using bioconductor software implemented in R
GSM399872 RMA algorithms using bioconductor software implemented in R
GSM399873 RMA algorithms using bioconductor software implemented in R
GSM399874 RMA algorithms using bioconductor software implemented in R
GSM399875 RMA algorithms using bioconductor software implemented in R
GSM399876 RMA algorithms using bioconductor software implemented in R
GSM399877 RMA algorithms using bioconductor software implemented in R
GSM399878 RMA algorithms using bioconductor software implemented in R
GSM399879 RMA algorithms using bioconductor software implemented in R
GSM399880 RMA algorithms using bioconductor software implemented in R
GSM399881 RMA algorithms using bioconductor software implemented in R
GSM399882 RMA algorithms using bioconductor software implemented in R
GSM399883 RMA algorithms using bioconductor software implemented in R
GSM399884 RMA algorithms using bioconductor software implemented in R
GSM399885 RMA algorithms using bioconductor software implemented in R
platform_id contact_name contact_email
GSM399864 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399865 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399866 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399867 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399868 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399869 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399870 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399871 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399872 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399873 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399874 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399875 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399876 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399877 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399878 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399879 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399880 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399881 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399882 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399883 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399884 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399885 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
contact_institute contact_address contact_city
GSM399864 Weizmann Inst. Hertzel Rehovot
GSM399865 Weizmann Inst. Hertzel Rehovot
GSM399866 Weizmann Inst. Hertzel Rehovot
GSM399867 Weizmann Inst. Hertzel Rehovot
GSM399868 Weizmann Inst. Hertzel Rehovot
GSM399869 Weizmann Inst. Hertzel Rehovot
GSM399870 Weizmann Inst. Hertzel Rehovot
GSM399871 Weizmann Inst. Hertzel Rehovot
GSM399872 Weizmann Inst. Hertzel Rehovot
GSM399873 Weizmann Inst. Hertzel Rehovot
GSM399874 Weizmann Inst. Hertzel Rehovot
GSM399875 Weizmann Inst. Hertzel Rehovot
GSM399876 Weizmann Inst. Hertzel Rehovot
GSM399877 Weizmann Inst. Hertzel Rehovot
GSM399878 Weizmann Inst. Hertzel Rehovot
GSM399879 Weizmann Inst. Hertzel Rehovot
GSM399880 Weizmann Inst. Hertzel Rehovot
GSM399881 Weizmann Inst. Hertzel Rehovot
GSM399882 Weizmann Inst. Hertzel Rehovot
GSM399883 Weizmann Inst. Hertzel Rehovot
GSM399884 Weizmann Inst. Hertzel Rehovot
GSM399885 Weizmann Inst. Hertzel Rehovot
contact_zip/postal_code contact_country
GSM399864 76100 Israel
GSM399865 76100 Israel
GSM399866 76100 Israel
GSM399867 76100 Israel
GSM399868 76100 Israel
GSM399869 76100 Israel
GSM399870 76100 Israel
GSM399871 76100 Israel
GSM399872 76100 Israel
GSM399873 76100 Israel
GSM399874 76100 Israel
GSM399875 76100 Israel
GSM399876 76100 Israel
GSM399877 76100 Israel
GSM399878 76100 Israel
GSM399879 76100 Israel
GSM399880 76100 Israel
GSM399881 76100 Israel
GSM399882 76100 Israel
GSM399883 76100 Israel
GSM399884 76100 Israel
GSM399885 76100 Israel
supplementary_file
GSM399864 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399864/GSM399864.CEL.gz
GSM399865 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399865/GSM399865.CEL.gz
GSM399866 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399866/GSM399866.CEL.gz
GSM399867 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399867/GSM399867.CEL.gz
GSM399868 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399868/GSM399868.CEL.gz
GSM399869 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399869/GSM399869.CEL.gz
GSM399870 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399870/GSM399870.CEL.gz
GSM399871 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399871/GSM399871.CEL.gz
GSM399872 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399872/GSM399872.CEL.gz
GSM399873 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399873/GSM399873.CEL.gz
GSM399874 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399874/GSM399874.CEL.gz
GSM399875 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399875/GSM399875.CEL.gz
GSM399876 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399876/GSM399876.CEL.gz
GSM399877 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399877/GSM399877.CEL.gz
GSM399878 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399878/GSM399878.CEL.gz
GSM399879 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399879/GSM399879.CEL.gz
GSM399880 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399880/GSM399880.CEL.gz
GSM399881 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399881/GSM399881.CEL.gz
GSM399882 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399882/GSM399882.CEL.gz
GSM399883 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399883/GSM399883.CEL.gz
GSM399884 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399884/GSM399884.CEL.gz
GSM399885 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399885/GSM399885.CEL.gz
data_row_count
GSM399864 10928
GSM399865 10928
GSM399866 10928
GSM399867 10928
GSM399868 10928
GSM399869 10928
GSM399870 10928
GSM399871 10928
GSM399872 10928
GSM399873 10928
GSM399874 10928
GSM399875 10928
GSM399876 10928
GSM399877 10928
GSM399878 10928
GSM399879 10928
GSM399880 10928
GSM399881 10928
GSM399882 10928
GSM399883 10928
GSM399884 10928
GSM399885 10928#gset@phenoData@data
experimental_design = gset@phenoData@data #These should contain experiment meta info
experimental_design[1:3,] title geo_accession status
GSM399864 Untreated, t0_a GSM399864 Public on Aug 07 2009
GSM399865 Untreated, t0_b GSM399865 Public on Aug 07 2009
GSM399866 Heat shock, t30 min GSM399866 Public on Aug 07 2009
submission_date last_update_date type channel_count
GSM399864 May 03 2009 Aug 07 2009 RNA 1
GSM399865 May 03 2009 Aug 07 2009 RNA 1
GSM399866 May 03 2009 Aug 07 2009 RNA 1
source_name_ch1 organism_ch1
GSM399864 Untreated S. cerevisiae cells Saccharomyces cerevisiae
GSM399865 Untreated S. cerevisiae cells Saccharomyces cerevisiae
GSM399866 heat treated S. cerevisiae cells Saccharomyces cerevisiae
characteristics_ch1 characteristics_ch1.1 characteristics_ch1.2
GSM399864 strain: 4741 stress: untreated time: 0 min
GSM399865 strain: 4741 stress: untreated time: 0 min
GSM399866 strain: 4741 stress: heat stress time: 30 min
treatment_protocol_ch1
GSM399864 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399865 At time 0 cells were treated with mild stresses and then transftered to another stress
GSM399866 At time 0 cells were treated with mild stresses and then transftered to another stress
growth_protocol_ch1
GSM399864 Cells were grown in YPD to mid log phase in 30 degrees
GSM399865 Cells were grown in YPD to mid log phase in 30 degrees
GSM399866 Cells were grown in YPD to mid log phase in 30 degrees
molecule_ch1
GSM399864 total RNA
GSM399865 total RNA
GSM399866 total RNA
extract_protocol_ch1
GSM399864 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399865 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
GSM399866 Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)
label_ch1
GSM399864 biotin
GSM399865 biotin
GSM399866 biotin
label_protocol_ch1
GSM399864 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399865 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
GSM399866 cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.
taxid_ch1 hyb_protocol
GSM399864 4932 According to standard Affymetrix protocol
GSM399865 4932 According to standard Affymetrix protocol
GSM399866 4932 According to standard Affymetrix protocol
scan_protocol
GSM399864 According to standard Affymetrix protocol
GSM399865 According to standard Affymetrix protocol
GSM399866 According to standard Affymetrix protocol
description
GSM399864 Gene expression in Rich media (reference sample)
GSM399865 Gene expression in Rich media (reference sample)
GSM399866 Gene expression in heat shock 40deg, 30min
data_processing
GSM399864 RMA algorithms using bioconductor software implemented in R
GSM399865 RMA algorithms using bioconductor software implemented in R
GSM399866 RMA algorithms using bioconductor software implemented in R
platform_id contact_name contact_email
GSM399864 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399865 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
GSM399866 GPL2529 Amir,,Mitchell amir.mitchell@weizmann.ac.il
contact_institute contact_address contact_city
GSM399864 Weizmann Inst. Hertzel Rehovot
GSM399865 Weizmann Inst. Hertzel Rehovot
GSM399866 Weizmann Inst. Hertzel Rehovot
contact_zip/postal_code contact_country
GSM399864 76100 Israel
GSM399865 76100 Israel
GSM399866 76100 Israel
supplementary_file
GSM399864 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399864/GSM399864.CEL.gz
GSM399865 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399865/GSM399865.CEL.gz
GSM399866 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM399nnn/GSM399866/GSM399866.CEL.gz
data_row_count
GSM399864 10928
GSM399865 10928
GSM399866 10928# gset@phenoData@varMetadata
# experimental_design[, "source_name_ch1"][1:10]
experimental_design[5:8, c("title", "source_name_ch1")] title source_name_ch1
GSM399868 Osmotic stress, t30 min KCl treated S. cerevisiae cells
GSM399869 Osmotic stress, t45 min KCl treated S. cerevisiae cells
GSM399870 Oxidative stress, t15 min H2O2 treated S. cerevisiae cells
GSM399871 Oxidative stress, t30 min H2O2 treated S. cerevisiae cellsexperimental_design$title## V2
## Untreated, t0_a
## V3
## Untreated, t0_b
## V4
## Heat shock, t30 min
## V5
## Heat shock, t45 min
## V6
## Osmotic stress, t30 min
## V7
## Osmotic stress, t45 min
## V8
## Oxidative stress, t15 min
## V9
## Oxidative stress, t30 min
## V10
## Oxidative stress, t45 min
## V11
## Oxidative stress, t90 min
## V12
## Oxidative stress (after heat shock), t15 min
## V13
## Oxidative stress (after heat shock), t30 min
## V14
## Oxidative stress (after heat shock), t45 min
## V15
## Oxidative stress (after heat shock), t90 min
## V16
## Rich media (after heat shock), t15 min
## V17
## Rich media (after heat shock), t45 min
## V18
## Oxidative stress (after osmotic stress), t15 min
## V19
## Oxidative stress (after osmotic stress), t30 min
## V20
## Oxidative stress (after osmotic stress), t45 min
## V21
## Oxidative stress (after osmotic stress), t90 min
## V22
## Rich media (after osmotic stress), t15 min
## V23
## Rich media (after osmotic stress), t45 min
## 22 Levels: Heat shock, t30 min ... Untreated, t0_bexperimental_design$title[grep("Oxidative stress, t", experimental_design$title)]## V8 V9
## Oxidative stress, t15 min Oxidative stress, t30 min
## V10 V11
## Oxidative stress, t45 min Oxidative stress, t90 min
## 22 Levels: Heat shock, t30 min ... Untreated, t0_bselected = c(1, 2, grep("Oxidative stress, t", experimental_design$title))
ex = ex[, selected]mylevels = c(0,0,15,30,45,90)
names(mylevels) = c("0","0", "15","30","45","90")
my.pvalues = numeric(length=length(ex[,1]))
registerDoMC(cores=4)
#my.pvalues = foreach( i = 1:100, .combine='rbind') %dopar% {
my.pvalues = foreach( i = 1:length(ex[,1]), .combine='rbind') %dopar% {
m = lm( ex[i,] ~ mylevels )
sm = summary(m)
pf(sm$fstatistic[1], sm$fstatistic[2], sm$fstatistic[3], lower.tail = FALSE)
}
row.names(my.pvalues) = row.names(gset@assayData$exprs)
head(my.pvalues)## value
## 1769308_at 0.2651722
## 1769309_at 0.8756291
## 1769310_at 0.8419849
## 1769311_at 0.1403187
## 1769312_at 0.7020425
## 1769313_at 0.5081199gpl <- annotation(gset)
platf <- getGEO(gpl, AnnotGPL=TRUE)## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error
## Warning in readLines(con, 1): seek on a gzfile connection returned an
## internal error## Warning in read.table(con, sep = sep, header = header, nrows =
## sampleRows, : seek on a gzfile connection returned an internal error
## Warning in read.table(con, sep = sep, header = header, nrows =
## sampleRows, : seek on a gzfile connection returned an internal error## Warning in read.table(file = file, header = header, sep = sep, quote =
## quote, : seek on a gzfile connection returned an internal errorncbifd <- data.frame(attr(dataTable(platf), "table"))
ncbifd[1:10,]## ID
## 1 1769308_at
## 2 1769309_at
## 3 1769310_at
## 4 1769311_at
## 5 1769312_at
## 6 1769313_at
## 7 1769314_at
## 8 1769315_at
## 9 1769316_s_at
## 10 1769317_at
## Gene.title
## 1 bifunctional hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase FOX2
## 2 histone H3 h3.3
## 3 notchless-like protein (predicted)
## 4 hypothetical protein
## 5 Pcl6p
## 6 Pkp2p
## 7 Pho8p
## 8 P-TEFb-associated cyclin-dependent protein kinase Cdk9
## 9 hypothetical protein///hypothetical protein///hypothetical protein///hypothetical protein
## 10 Dat1p
## Gene.symbol
## 1 FOX2
## 2 hht3
## 3 SPCC18.05c
## 4 YDL157C
## 5 PCL6
## 6 PKP2
## 7 PHO8
## 8 cdk9
## 9 SPAC977.01///SPBC1348.02///SPAC750.05c///SPBPB2B2.19c
## 10 DAT1
## Gene.ID UniGene.title UniGene.symbol
## 1 853878 <NA> <NA>
## 2 2539804 <NA> <NA>
## 3 2539380 <NA> <NA>
## 4 851398 <NA> <NA>
## 5 856787 <NA> <NA>
## 6 852821 <NA> <NA>
## 7 852092 <NA> <NA>
## 8 2540239 <NA> <NA>
## 9 2543353///2541576///2541564///2541343 <NA> <NA>
## 10 854927 <NA> <NA>
## UniGene.ID Nucleotide.Title GI GenBank.Accession Platform_CLONEID
## 1 <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA>
## 4 <NA> <NA> <NA> <NA> <NA>
## 5 <NA> <NA> <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA>
## 9 <NA> <NA> <NA> <NA> <NA>
## 10 <NA> <NA> <NA> <NA> <NA>
## Platform_ORF Platform_SPOTID Chromosome.location
## 1 YKR009C <NA> <NA>
## 2 SPBC1105.11c <NA> <NA>
## 3 SPCC18.05c <NA> <NA>
## 4 YDL157C <NA> <NA>
## 5 YER059W <NA> <NA>
## 6 YGL059W <NA> <NA>
## 7 YDR481C <NA> <NA>
## 8 SPBC32H8.10 <NA> <NA>
## 9 SPAC750.05c <NA> <NA>
## 10 YML113W <NA> <NA>
## Chromosome.annotation
## 1 Chromosome XI, NC_001143.9 (454352..457054, complement)
## 2 Chromosome II, NC_003423.3 (3528800..3529657, complement)
## 3 Chromosome III, NC_003421.2 (1962945..1964811, complement)
## 4 Chromosome IV, NC_001136.10 (174232..174588, complement)
## 5 Chromosome V, NC_001137.3 (272624..273886)
## 6 Chromosome VII, NC_001139.9 (392223..393698)
## 7 Chromosome IV, NC_001136.10 (1418550..1420250, complement)
## 8 Chromosome II, NC_003423.3 (1470513..1473182)
## 9 Chromosome I, NC_003424.3 (29764..31069)///Chromosome II, NC_003423.3 (7633..9457)///Chromosome I, NC_003424.3 (5565881..5567337, complement)///Chromosome II, NC_003423.3 (4503653..4505257, complement)
## 10 Chromosome XIII, NC_001145.3 (44045..44791)
## GO.Function
## 1 3-hydroxyacyl-CoA dehydrogenase activity///catalytic activity///enoyl-CoA hydratase activity///isomerase activity///lyase activity///oxidoreductase activity///oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## 2 DNA binding///protein binding///protein heterodimerization activity
## 3 molecular_function
## 4 molecular_function
## 5 cyclin-dependent protein serine/threonine kinase regulator activity///protein kinase binding
## 6 ATP binding///kinase activity///nucleotide binding///protein kinase activity///protein serine/threonine kinase activity///pyruvate dehydrogenase (acetyl-transferring) kinase activity///pyruvate dehydrogenase (acetyl-transferring) kinase activity///transferase activity
## 7 alkaline phosphatase activity///alkaline phosphatase activity///catalytic activity///fructose-2,6-bisphosphate 6-phosphatase activity///hydrolase activity///metal ion binding///phosphatase activity
## 8 ATP binding///RNA polymerase II carboxy-terminal domain kinase activity///cyclin-dependent protein serine/threonine kinase activity///protein binding///protein serine/threonine kinase activity
## 9 molecular_function///molecular_function///molecular_function///molecular_function
## 10 AT DNA binding///DNA binding
## GO.Process
## 1 fatty acid beta-oxidation///fatty acid beta-oxidation///fatty acid metabolic process///lipid metabolic process///metabolic process///oxidation-reduction process
## 2 cellular response to DNA damage stimulus///cellular response to DNA damage stimulus///chromatin assembly or disassembly
## 3 ribosome biogenesis
## 4 biological_process
## 5 carbohydrate metabolic process///glycogen metabolic process///regulation of cyclin-dependent protein serine/threonine kinase activity///regulation of glycogen biosynthetic process///regulation of glycogen catabolic process
## 6 carbohydrate metabolic process///carbon utilization///glucose metabolic process///negative regulation of catalytic activity///peptidyl-serine phosphorylation///phosphorylation///protein phosphorylation
## 7 metabolic process///nicotinamide nucleotide metabolic process///protein dephosphorylation
## 8 phosphorylation of RNA polymerase II C-terminal domain///regulation of transcription elongation from RNA polymerase II promoter///transcription from RNA polymerase I promoter
## 9 biological_process///biological_process///biological_process///biological_process
## 10 negative regulation of transcription from RNA polymerase II promoter
## GO.Component
## 1 peroxisome///peroxisome
## 2 mating-type region heterochromatin///nuclear nucleosome///nuclear pericentric heterochromatin///nuclear telomeric heterochromatin
## 3 nucleolus///nucleus///protein complex
## 4 mitochondrion///mitochondrion
## 5 cyclin-dependent protein kinase holoenzyme complex///cytoplasm///nucleus
## 6 mitochondrial matrix///mitochondrion///mitochondrion
## 7 cytoplasm///fungal-type vacuole membrane///integral component of membrane///membrane///vacuolar membrane///vacuole
## 8 P-TEFb-cap methyltransferase complex///nucleus///positive transcription elongation factor complex b
## 9 cell surface///cell surface///endoplasmic reticulum///integral component of membrane///cell surface///endoplasmic reticulum///integral component of membrane///membrane
## 10 cytosol///nucleus
## GO.Function.ID
## 1 GO:0003857///GO:0003824///GO:0004300///GO:0016853///GO:0016829///GO:0016491///GO:0016616
## 2 GO:0003677///GO:0005515///GO:0046982
## 3 GO:0003674
## 4 GO:0003674
## 5 GO:0016538///GO:0019901
## 6 GO:0005524///GO:0016301///GO:0000166///GO:0004672///GO:0004674///GO:0004740///GO:0004740///GO:0016740
## 7 GO:0004035///GO:0004035///GO:0003824///GO:0047386///GO:0016787///GO:0046872///GO:0016791
## 8 GO:0005524///GO:0008353///GO:0004693///GO:0005515///GO:0004674
## 9 GO:0003674///GO:0003674///GO:0003674///GO:0003674
## 10 GO:0003680///GO:0003677
## GO.Process.ID
## 1 GO:0006635///GO:0006635///GO:0006631///GO:0006629///GO:0008152///GO:0055114
## 2 GO:0006974///GO:0006974///GO:0006333
## 3 GO:0042254
## 4 GO:0008150
## 5 GO:0005975///GO:0005977///GO:0000079///GO:0005979///GO:0005981
## 6 GO:0005975///GO:0015976///GO:0006006///GO:0043086///GO:0018105///GO:0016310///GO:0006468
## 7 GO:0008152///GO:0046496///GO:0006470
## 8 GO:0070816///GO:0034243///GO:0006360
## 9 GO:0008150///GO:0008150///GO:0008150///GO:0008150
## 10 GO:0000122
## GO.Component.ID
## 1 GO:0005777///GO:0005777
## 2 GO:0031934///GO:0000788///GO:0031618///GO:0005724
## 3 GO:0005730///GO:0005634///GO:0043234
## 4 GO:0005739///GO:0005739
## 5 GO:0000307///GO:0005737///GO:0005634
## 6 GO:0005759///GO:0005739///GO:0005739
## 7 GO:0005737///GO:0000329///GO:0016021///GO:0016020///GO:0005774///GO:0005773
## 8 GO:0070693///GO:0005634///GO:0008024
## 9 GO:0009986///GO:0009986///GO:0005783///GO:0016021///GO:0009986///GO:0005783///GO:0016021///GO:0016020
## 10 GO:0005829///GO:0005634my.pvalues.BH = p.adjust(my.pvalues, "BH")
names(my.pvalues.BH) = row.names(gset@assayData$exprs)
hist(my.pvalues.BH)
sig= my.pvalues.BH[my.pvalues.BH < 0.05]
sig= data.frame(sig)
sig$ID = row.names(sig)
#ncbifd[ match(names(sig), as.character( ncbifd$ID) ), ]
sig2 = merge(sig, ncbifd, by="ID")
sig2 ID sig Gene.title
1 1774675_at 0.02881499 ribonucleotide-diphosphate reductase subunit RNR2
Gene.symbol Gene.ID UniGene.title UniGene.symbol UniGene.ID
1 RNR2 853427
Nucleotide.Title GI GenBank.Accession Platform_CLONEID Platform_ORF
1 YJL026W
Platform_SPOTID Chromosome.location
1
Chromosome.annotation
1 Chromosome X, NC_001142.9 (392404..393603)
GO.Function
1 metal ion binding///oxidoreductase activity///ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor///contributes_to ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor///ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO.Process
1 DNA replication///deoxyribonucleoside diphosphate metabolic process///deoxyribonucleotide biosynthetic process///oxidation-reduction process
GO.Component
1 cytoplasm///nucleus///nucleus///ribonucleoside-diphosphate reductase complex
GO.Function.ID
1 GO:0046872///GO:0016491///GO:0004748///contributes_to GO:0004748///GO:0004748
GO.Process.ID
1 GO:0006260///GO:0009186///GO:0009263///GO:0055114
GO.Component.ID
1 GO:0005737///GO:0005634///GO:0005634///GO:0005971
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