Accumulation of genomic data is critical to our understanding of the overall functionality of a species. To facilitate designing microarray experiments for poorly-studied yeast species, we developed this system to recommend the most informative experiments based on available
Saccharomyces cerevisiae data. The recommendation of the experiments is based on the following three factors:
Overall accuracy of an experiment in capturing protein functions.
Overlap between different experiments represented by their conditional mutual information.
Existing list of experiments in the poorly-studied yeast species.
Here, α∈[0,1] represents the trade-off between accuracy and overlap of the datasets. When α=1, we recommend experiments only based on their individual accuracy; and when α=0, we recommend experiments only based on their similarity from existing datasets. An α between 0.3 and 0.9 is usually preferred, depending on the purpose of your experiments (whether to achieve accuracy in integration or achieving accuracy in function prediction).
Experiment Description Pubmed ID # of arrays Causton01_heat
heat response 11179418 7 Yvert03_orig
Trans-acting regulatory variation 12897782 90 Jelinsky00
Exposure to alkylating, oxidizing agents, ionizing radiation 11027285 28 Brauer05_batch1
Diauxic shift time course (Batch1) 15758028 13 Pitkanen04
Phosphomannose isomerase PMI40 deletion strain response to excess mannose 15520001 15 Duvel03_delayedRap
post heat shock, delayed rapamycin exposure time course 12820961 20 Brem05_orig
Genetic variation in gene expression among parents and progenies 15659551 131 Takagi05
Ssl1 mutant for a subunit of TFIIH response to methyl methanesulfonate 15837426 12 Tai05
Nutrient limitation under aerobic and anaerobic conditions 15496405 24 Chitikila02
TBP inhibition 12419230 20 Schawalder04
IFH1 overexpression: time course 15616569 24 Brem02_set1
Transcriptional regulation (I) 11923494 40 Yeang05
Transcription factor deletions 15998451 7 ORourke03
HOG MAPK pathway 14595107 133 Bedalov01
splitomicin exposure and sir2 mutants 11752457 7 Rudra05
fhl1 and ifh1 deletion mutants 15692568 6 Jin04
Xylose metabolism 15528549 6 Yvert03_dyeSwap
Trans-acting regulatory variation (dye swap) 12897782 90 Ogawa00_set1
Phosphate-regulated pathway (I) 11102525 5 Bernstein00_HDACsin3sap30ume6hda1hos2hos3
Histone deacetylase (sin3/sap30/ume6/hda1/hos2/hos3 deletions) 11095743 7 Pramila06
0 Epstein00
Mitochondrial dysfunction 11179416 11 Roberts00
Pheremone response 10657304 56 Brem02_set2dyeSwap
Transcriptional regulation (II)(dye swap) 11923494 11 Causton01_acid
acid response 11179418 11 Gasch00_menadione
Menadione exposure time course 11102521 9 Causton01_peroxide
peroxide response 11179418 7 Causton01_NaCl
NaCl response 11179418 6 Yoshimoto02_Ca
Ca(2+) exposure 12058033 24 Orlandi04
Deubiquitinating enzyme UBP10 inactivation 14623890 4 Keller01
Haa1 analysis 11504737 4 Gasch00_hypo-osmotic
Hypo-osmotic shock time course 11102521 5 CarmelHarel01
H2O2 exposure to wt and Deltatrr1 knockout 11169101 15 Gasch00_DTT_y13
0 Duvel03_immediateRap
post heat shock, immediate rapamycin exposure time course 12820961 10 Saldanha04_LeucineBatchChem
limitation by Leucine 15240820 29 Sabet04
Histone deacetylase RPD3 deletion and histone mutations 15456858 18 Brem02_set2
Transcriptional regulation (II) 11923494 12 Caba05
Genotoxic stress 15878181 24 Gasch00_diamideTreatment
Diamide treatment time course 11102521 8 Huang02
pho85 related knockouts 12077337 20 Gross00
Copper regulon 10922376 6 Gasch00_hyper-osmotic
Hyper-osmotic shock time course 11102521 6 Brem02_set1dyeSwap
Transcriptional regulation (I)(dye swap) 11923494 40 Prinz04
Filamentous-form growth on solid media time course 14993204 10 Leber04
Unfolded protein response and HAC1 transcription 15314654 13 Spellman98_alphaFactor
Cell cycle, alpha-factor block-release 9843569 16 Lee05
rnt1 null mutant expression profile 15989963 9 Brem05_dyeSwap
Genetic variation in gene expression among parents and progenies (dye-swap) 15659551 131 ShakouryElizeh04
Iron deprivation 14668481 6 Chu98
Sporulation time course 9784122 7 Primig00
Sporulation of two strains 11101837 24 Saldanha04_UracilBatchChem
limitation by Uracil 15240820 20 Miyake04
abf1-1 mutant at 36C 15192094 4 Madhani99
MAPK mutants 10535956 11 Boer05
leu3 mutant expression profiles 15949974 12 RodriguezNavarro04
sus1 mutant 14718168 6 Olesen02
Fermentation time course 12702272 12 Martin04
TOR2-controlled transcription 15476558 12 Lyons00
Zinc homeostatis, zap1 10884426 9 Carroll01
pho85 inhibition 11675494 12 Fleming99
proteasome inhibition with exposure to PS-341 11830665 30 Belli04
Oxidative stress and glutaredoxin 5-deficient mutant 14722110 9 transfer_of_w.t._to_YPA
0 Spellman98_cdc15
Cell cycle, cdc15 block-release 9843569 25 Gasch00_HSto37
Heat Shock from various temp to 37C 11102521 6 Saldanha04_PhosphateBatchChem
limitation by Phosphate 15240820 30 Brauer05_batch2
Diauxic shift time course (Batch2) 15758028 7 Gasch00_HS25-37
Heat Shock 25C to 37C time course 11102521 8 Pramila06_10min
0 transfer_of_w.t._to_glucose
0 Spellman98_elutriation
Cell cycle, elutriation 9843569 14 DeRisi97
Diauxic shift time course 9381177 7 Robertson00
TPK1, TPK2, TPK3 mutants 10811893 12 Cho98
mitotic cell cycle 9702192 17 Eriksson05
SPT10 global transcription regulator null mutant 16199888 6 transfer_of_pSPS4-NDT80_to_YPD
0 Bernstein00_HDACrpd3sin3hda1
Histone deacetylase (rpd3/sin3/hda1 deletions) 11095743 6 Cohen02
yap1 and yap2 knockouts with peroxide and cadmium added 12006656 11 Gasch00_HS37-25
Heat Shock 37C to 25C 11102521 5 Ideker01
GAL mutants 11340206 21 Baetz01
slt2/swi4/swi6/bck1 knockouts 11533240 5 Gasch00_adenineStarvation
Amino acid, adenine starvation 11102521 5 Causton01_alkali
alkali response 11179418 8 glucose_glycerol_transition
0 Segal03_stationaryPhaseYPL230W
Stationary phase, ypl230w mutant 12740579 12 deNadal04
Osmotic stress 14737171 12 Lopez00
gcr1 mutant, glucose exposure 10940042 17 Gasch00_stationaryPhase_y14
0 Marton98
immunosuppressant response 9809554 7 Gasch00_DTT_y14
0 Gasch00_steadyState_y13
0 Yun00
Iron uptake 10744769 4 Ogawa00_set2
Phosphate-regulated pathway (II) 11102525 3 Hughes00
diverse knockout mutants 10929718 300 Fry03
Aging in yeast 12875747 8 Saldanha04_UraSulPhoLeuComp
comparison of limitation by Ura, Sul, Pho, and Leu 15240820 24 Saldanha04_SulfateBatchChem
limitation by Sulfate 15240820 21 Segal03_hypo-osmoticPpt1
Hypo-osmotic shock, ppt1 mutant 12740579 10 Jones03_dyeSwap
Ras/cAMP signal transduction pathway (dye swap) 14570984 5 Bulik03
Chitin synthesis 14555471 11 Yoshimoto02_Na
Na(+) exposure 12058033 16 Gasch00_steadyState_y14
0 Sapra04
Pre-mRNA splicing factor mutants at restrictive temperature time course 15452114 24 Causton01_sorbitol
Sorbitol response 11179418 6 Gasch00_HOtimeCourse
Hydrogen peroxide response time course 11102521 9 Gasch00_HS29-33
Heat Shock 29C to 33C time course 11102521 4 Segal03_HSkin82
Heat Shock, kin82 mutant 12740579 10 Gasch00_HS30-37
Heat Shock 30C to 37C time course 11102521 5 Bro03
Lithium response 12791685 7 Protchenko01
Iron concentration and AFT1 overexpression 11673473 4 Jones03_orig
Ras/cAMP signal transduction pathway 14570984 5 transfer_of_w.t._to_YPD
0 Gasch00_stationaryPhase_y12
0 Yamamoto05
Heat shock transcription factor 1 mutant response to heat stress 15647283 4 Sudarsanam00_set2
Snf/Swi mutants (384_F_v1.0) 10725359 8 Pramila06swap
0 Ferea99
Evolved strains 10449761 4 Gasch00_carbonSources
Carbon sources 11102521 6 Gasch00_Ndepletion
Nitrogen depletion time course 11102521 9 Shapira04
oxidative stress responses 15371544 70 Bernstein00_TSA
Trichostatin A treatment time course 11095743 5 Hardwick00
rapamycin exposure 10611304 14 Angus01
rsc3/rsc30 knockouts 11336698 8 Gasch00_HSmild
Mild Heat Shock 11102521 6