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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
Matrices@CSB.DB: S.cerevisiae Matrix Information Page
This page provides background information about the Saccharomyces cerevisiae gene expression data matrices which are the basis for the co-response analyses. For further information about particular experiments follow the given link.
S.cerevisiae Matrices
To get information of your choice for the Saccharomyces cerevisiae gene expression data matrices use the links listed below.
Matrix smd0511: Processing

Saccharomyces cerevisiae - Expression Data Matrix smd0511 (m0511): Processing back to top

Transcript profiles of Matrix smd0511 (m0511) were derived from the Stanford Microarray Database (SMD, Sherlock et al., 2001). Gene expression was analysed by colour-coded cDNA hybridisation technology. The transcript profiling experiments of smd0511 (m0511) covered miscellaneous treatments. Individual spots were quality checked as recommended by the SMD tutorial. In order to reduce the number of missing data smd0511 (m0511) was designed to maximise the number of experiments. Matrix smd0511 (m0511) comprised 48 experiments and is described by 4848 genes. To avoid overrepresentation of experimental conditions the chosen number of replicates per experimental condition was approximately equal. Normalised gene expression ratios (Rat2N) were log base 2 transformed. Co-Response analyses were performed on range normalised (genes) matrix.
For detailed description of the experiments please query the Stanford Microarray Database (SMD). You can search for details via SMD.ID (Stanford Experiment ID), by Experimenter or Category etc.
Matrix smd0511 : Experiments

Saccharomyces cerevisiae - Expression Data Matrix smd0511 (m0511): Experiment List back to top

For detailed description of the experiments please query the Stanford Microarray Database (SMD). You can search for details via SMD.ID (Stanford Experiment ID), by Experimenter or Category etc.
CSB.DB ID SMD.ID Group Description SMD Category SMD Sub-Category Experimenter
130 13064 4 wt/crz1 Ca 30min (2) calcium Transcription Factors CYERT
147 651 5 alpha factor release sample019 Cell-cycle Alpha factor block-release SPELLMAN
151 1107 alpha factor release sample025
153 1673 alpha factor release sample021
157 650 alpha factor release sample017
183 9837 7 CLB2 induction 40minutes (possible against CLB5 0min) Cell-cycle Cell-cycle factors SPELLMAN
185 9838 CLN3 induction 30 minutes
190 53 8 Elutriation2:Sample2:Time2.0hrs Cell-cycle Elutriation SPELLMAN
191 55 Elutriation2:Sample2:Time3.0hrs
192 57 Elutriation2:Sample2:Time4.0hrs
195 1674 Elutriation2:Sample2:Time5.5hrs
250 14081 11 FY2(B) vs. FY2(A) 23.5 hours Chemostat Control experiment BRAUER
261 5061 12 SWI4 3xHA IP with anti-HA, alpha-factor treated cells, G-array Chromatin IP Cell-cycle factors VISHY
265 5045 SWI4 IP with anti-HA, alpha-factor treated cells, G-array
313 5237 16 DES460 (wt) - mock irradiation - 5 min DNA damage Gamma radiation AGASCH
316 5242 DES460 (wt) - mock irradiation - 90 min
318 5244 DES459 (mec1) - mock irradiation -15 min
331 5246 DES459 (mec1) - mock irradiation - 60 min
442 30463 23 Pomona/Brown pol2-12 red GCAT Mutant CAMPBELL
443 30773 Pomona/Brown Sir3x red
482 8685 29 20 uM Fe vs 100 uM Fe: met Martel Martel FEREA
502 3020 31 WT vs lpz8 null cells in high Cu Metals Copper ERAY
505 12169 32 aft2 minus cells with control plasmid vs aft2 minus cells with AFT2 vector Metals Transcription Factors ERAY
550 33777 36 delYPL230w_stationary_phase_0hours Mutants YPD-stationary-phase MICHAS
615 1173 39 PHO4c vs. wild type Phosphate Nutrient limitation NOGAWA
637 11420 40 BY4741#3 fract11 Polysomes wild-type ARAVAY
642 11467 BY4741#3 fract3
648 11415 BY4741#3 fract6
714 12016 43 rpb1_50min_random_3rd RNA processing RNA stability YULEI
716 12012 rpb1_20min_random_3rd
717 12014 rpb1_30min_random_3rd
718 12015 rpb1_40min_random_3rd
725 12019 rpb1_0minb_random_3rd
726 12017 rpb1_60min_random_3rd
734 12025 rpb1_0mina_dT_3rd
743 6400 rpb1_15min_random_1st
746 12052 rpb1_5min_random_3rd
756 7759 45 Na 30min salt treatment Time course CYERT
759 7762 Na+FK 15min
760 7763 Na+FK 30min
761 7764 Na+FK 45min
772 6854 48 Early Sporulation ndt80 delete Sporulation Transcription Factors JDERISI
773 6856 Sporulation t30min
775 6826 Sporulation t2hrs
776 6859 Mid-Sporulation ndt80 delete
925 4047 61 0.8M NaCl +FK506 - 15 min Stress salt treatment, unspecified AGASCH
926 4048 0.8M NaCl +FK506 - 30 min
980 16338 69 DES460 vs. DES460 YPD log phase control Yeast expression Control experiment AGASCH

For suggestions and questions feel free to contact the CSB.DB curator.
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