CSB.DB: Matrix

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 (m0511): processing | experiments |

Matrix smd0511: Processing

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

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

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	7	CLN3 induction 30 minutes	Cell-cycle	Cell-cycle factors	SPELLMAN
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	12	SWI4 IP with anti-HA, alpha-factor treated cells, G-array	Chromatin IP	Cell-cycle factors	VISHY
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	23	Pomona/Brown Sir3x red	GCAT	Mutant	CAMPBELL
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	61	0.8M NaCl +FK506 - 30 min	Stress	salt treatment, unspecified	AGASCH
980	16338	69	DES460 vs. DES460 YPD log phase control	Yeast expression	Control experiment	AGASCH