Thursday, March 31, 2016

Thalassemia

Thalassemia module References






Oakridge health data science

Dr. Georgia Tourassi
Director of the Biomedical Sciences and Engineering Center
and the Health Data Sciences Institute

OAK RIDGE NATIONAL LABORATORY

Thursday, March 31, 2016
University Center/Raccoon Mountain Room
11:00 AM – 12:00 PM

The Quantified Human:  A Data-driven Systems Approach To Understand, Predict and Improve Health Outcomes
Abstract: The mission of a National lab is to enable scientific innovations and transformative technical breakthroughs for grand challenges by leveraging unique resources and principles of trans-disciplinary collaboration. Oak Ridge National Laboratory (ORNL) is taking on the ‘Big Data to Knowledge’ challenge for health innovations via its Health Data Sciences Institute (HDSI). In this presentation I will describe HDSI’s vision and related activities to create the “quantified human”, a computational framework that supports a multi-scale systems approach to understand, predict, and improve health outcomes for individuals and populations. I will discuss the framework in the context of the National Cancer Surveillance program to improve cancer outcomes in the real world.
Short Bio: Dr. Georgia Tourassi is the Director of the Biomedical Science and Engineering Center and the Health Data Sciences Institute at the Oak Ridge National Laboratory (ORNL). She holds a B.S. in Physics from the University of Thessaloniki, Greece (1987) and a Ph.D. in Biomedical Engineering from Duke University (1993). She received the Young Investigator's Award from NIH (1994) and the Whitaker Foundation (1996). Before joining ORNL, Dr. Tourassi was Professor of Radiology and the Medical Physics Graduate Program at Duke University Medical Center, where she currently holds an Adjunct Professor position. Her research interests include biomedical informatics, medical imaging, and computer-aided decision support. Her medical imaging research has been featured in several publications including The Economist and recently won an R&D 100 award. Latest research work is focused on the use of cyber-informatics for cancer related epidemiological discovery. Her research has been funded by NIH; DOD; DOE; and the Komen and Whitaker Foundations. She has authored over 250 peer-reviewed journals, conference proceedings papers, and book chapters. She serves regularly on NIH grant review study sections (Charter member for BMIT 2007-2011 and BCHI 2014-now. She also serves on the FDA advisory committee on computer-aided diagnosis devices. She is a senior member of IEEE, INNS, and SPIE. In 2014 she won an R&D 100 Award and in 2015 she was elected Fellow of the American Institute of Medical and Biological Engineering (AIMBE) and the American Association of Physicists in Medicine (AAPM).


bio325 guest lectures

Guest lectures in Evolution in Action, BIO325, Spelman College, Spring 2016, 

March 31 Thu, 

1. Install R and RStudio. 
Step1:   Instructions to download R. 
Step2:   Install R studio.  For more information, see 
http://hongqinlab.blogspot.com/2015/01/rrstudio-tutorial-page-for-bio125.html

2. Download computer exercises codes and files
https://github.com/hongqin/bio325.sp16


3. Microarray and gene expression profiling  

https://en.wikipedia.org/wiki/DNA_microarray

https://en.wikipedia.org/wiki/Gene_expression_profiling

https://en.wikipedia.org/wiki/Hierarchical_clustering

4.  Clustering demo using a picture (Student group exercise)
Reshuffle pixels in a picture to demonstrate the utility of clustering.

Students will need to install HeatPlus, adimpro, and pixmap packages. 

April 5 Tue

5. Data analysis exercise
Expression data from S. cerevisiae under serial stresses, including H2O2 time course

Reference:  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15936
 http://www.ncbi.nlm.nih.gov/pubmed/19536156


Wednesday, March 30, 2016

bio125, 20160330Tue exercises, gene regulations


Section 3:
Review gene regulation 1,2,3,4. The spent 30 minutes on APE 11. Show a student video as demo.

Section 4.
Did most of the talk and the 4 exercises in 1.5 hours. Then let students work on APE11.

Tuesday, March 29, 2016

H2O2 time course expression data, GEO

Expression data from S. cerevisiae under serial stresses GSE15936 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15936
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)
Load series and platform data from GEO After retrieve it from NCBI GEO, ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15936/matrix/ Qin saved the data locally for in-class exercises.
 gset <- getGEO(filename="GSE15936_series_matrix.txt.gz")
## File stored at:
## /var/folders/nl/4nhwcdy107z85j39348mvctm0000gp/T//RtmpxcFHA4/GPL2529.soft
get expression matrix
ex <- exprs(gset)
Normalize them by total intensity
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 
##         1
apply( 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 
##  6.051965
boxplot( ex )
What is boxplot? See http://tinyurl.com/zw7bd9j
Study 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 0
gset@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
Find the experimental design information
#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 cells
Pick oxidative stress time course
experimental_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_b
experimental_design$title[grep("Oxidative stress, t", experimental_design$title)]
##                        V8                        V9 
## Oxidative stress, t15 min Oxidative stress, t30 min 
##                       V10                       V11 
## Oxidative stress, t45 min Oxidative stress, t90 min 
## 22 Levels: Heat shock, t30 min ... Untreated, t0_b
selected = c(1, 2, grep("Oxidative stress, t", experimental_design$title))
ex = ex[, selected]
Regression for H2O2 time dependent changes
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 0.5081199
Load NCBI platform annotation
gpl <- 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 error
ncbifd <- 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:0005634
pick significant genes
my.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