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:
  1. Overall accuracy of an experiment in capturing protein functions.
  2. Overlap between different experiments represented by their conditional mutual information.
  3. 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).
Please input α∈[0,1] and select the existing datasets of your species:
ExperimentDescriptionPubmed ID# of arrays
Causton01_heat   heat response111794187
Yvert03_orig   Trans-acting regulatory variation1289778290
Jelinsky00   Exposure to alkylating, oxidizing agents, ionizing radiation1102728528
Brauer05_batch1   Diauxic shift time course (Batch1)1575802813
Pitkanen04   Phosphomannose isomerase PMI40 deletion strain response to excess mannose1552000115
Duvel03_delayedRap   post heat shock, delayed rapamycin exposure time course1282096120
Brem05_orig   Genetic variation in gene expression among parents and progenies15659551131
Takagi05   Ssl1 mutant for a subunit of TFIIH response to methyl methanesulfonate1583742612
Tai05   Nutrient limitation under aerobic and anaerobic conditions1549640524
Chitikila02   TBP inhibition1241923020
Schawalder04   IFH1 overexpression: time course1561656924
Brem02_set1   Transcriptional regulation (I)1192349440
Yeang05   Transcription factor deletions159984517
ORourke03   HOG MAPK pathway14595107133
Bedalov01   splitomicin exposure and sir2 mutants117524577
Rudra05   fhl1 and ifh1 deletion mutants156925686
Jin04   Xylose metabolism155285496
Yvert03_dyeSwap   Trans-acting regulatory variation (dye swap)1289778290
Ogawa00_set1   Phosphate-regulated pathway (I)111025255
Bernstein00_HDACsin3sap30ume6hda1hos2hos3   Histone deacetylase (sin3/sap30/ume6/hda1/hos2/hos3 deletions)110957437
Pramila06   0
Epstein00   Mitochondrial dysfunction1117941611
Roberts00   Pheremone response1065730456
Brem02_set2dyeSwap   Transcriptional regulation (II)(dye swap)1192349411
Causton01_acid   acid response1117941811
Gasch00_menadione   Menadione exposure time course111025219
Causton01_peroxide   peroxide response111794187
Causton01_NaCl   NaCl response111794186
Yoshimoto02_Ca   Ca(2+) exposure1205803324
Orlandi04   Deubiquitinating enzyme UBP10 inactivation146238904
Keller01   Haa1 analysis115047374
Gasch00_hypo-osmotic   Hypo-osmotic shock time course111025215
CarmelHarel01   H2O2 exposure to wt and Deltatrr1 knockout1116910115
Gasch00_DTT_y13   0
Duvel03_immediateRap   post heat shock, immediate rapamycin exposure time course1282096110
Saldanha04_LeucineBatchChem   limitation by Leucine1524082029
Sabet04   Histone deacetylase RPD3 deletion and histone mutations1545685818
Brem02_set2   Transcriptional regulation (II)1192349412
Caba05   Genotoxic stress1587818124
Gasch00_diamideTreatment   Diamide treatment time course111025218
Huang02   pho85 related knockouts1207733720
Gross00   Copper regulon109223766
Gasch00_hyper-osmotic   Hyper-osmotic shock time course111025216
Brem02_set1dyeSwap   Transcriptional regulation (I)(dye swap)1192349440
Prinz04   Filamentous-form growth on solid media time course1499320410
Leber04   Unfolded protein response and HAC1 transcription1531465413
Spellman98_alphaFactor   Cell cycle, alpha-factor block-release984356916
Lee05   rnt1 null mutant expression profile159899639
Brem05_dyeSwap   Genetic variation in gene expression among parents and progenies (dye-swap)15659551131
ShakouryElizeh04   Iron deprivation146684816
Chu98   Sporulation time course97841227
Primig00   Sporulation of two strains1110183724
Saldanha04_UracilBatchChem   limitation by Uracil1524082020
Miyake04   abf1-1 mutant at 36C151920944
Madhani99   MAPK mutants1053595611
Boer05   leu3 mutant expression profiles1594997412
RodriguezNavarro04   sus1 mutant147181686
Olesen02   Fermentation time course1270227212
Martin04   TOR2-controlled transcription1547655812
Lyons00   Zinc homeostatis, zap1108844269
Carroll01   pho85 inhibition1167549412
Fleming99   proteasome inhibition with exposure to PS-3411183066530
Belli04   Oxidative stress and glutaredoxin 5-deficient mutant147221109
transfer_of_w.t._to_YPA   0
Spellman98_cdc15   Cell cycle, cdc15 block-release984356925
Gasch00_HSto37   Heat Shock from various temp to 37C111025216
Saldanha04_PhosphateBatchChem   limitation by Phosphate1524082030
Brauer05_batch2   Diauxic shift time course (Batch2)157580287
Gasch00_HS25-37   Heat Shock 25C to 37C time course111025218
Pramila06_10min   0
transfer_of_w.t._to_glucose   0
Spellman98_elutriation   Cell cycle, elutriation984356914
DeRisi97   Diauxic shift time course93811777
Robertson00   TPK1, TPK2, TPK3 mutants1081189312
Cho98   mitotic cell cycle970219217
Eriksson05   SPT10 global transcription regulator null mutant161998886
transfer_of_pSPS4-NDT80_to_YPD   0
Bernstein00_HDACrpd3sin3hda1   Histone deacetylase (rpd3/sin3/hda1 deletions)110957436
Cohen02   yap1 and yap2 knockouts with peroxide and cadmium added1200665611
Gasch00_HS37-25   Heat Shock 37C to 25C111025215
Ideker01   GAL mutants1134020621
Baetz01   slt2/swi4/swi6/bck1 knockouts115332405
Gasch00_adenineStarvation   Amino acid, adenine starvation 111025215
Causton01_alkali   alkali response111794188
glucose_glycerol_transition   0
Segal03_stationaryPhaseYPL230W   Stationary phase, ypl230w mutant1274057912
deNadal04   Osmotic stress1473717112
Lopez00   gcr1 mutant, glucose exposure1094004217
Gasch00_stationaryPhase_y14   0
Marton98   immunosuppressant response98095547
Gasch00_DTT_y14   0
Gasch00_steadyState_y13   0
Yun00   Iron uptake107447694
Ogawa00_set2   Phosphate-regulated pathway (II)111025253
Hughes00   diverse knockout mutants10929718300
Fry03   Aging in yeast128757478
Saldanha04_UraSulPhoLeuComp   comparison of limitation by Ura, Sul, Pho, and Leu1524082024
Saldanha04_SulfateBatchChem   limitation by Sulfate1524082021
Segal03_hypo-osmoticPpt1   Hypo-osmotic shock, ppt1 mutant1274057910
Jones03_dyeSwap   Ras/cAMP signal transduction pathway (dye swap)145709845
Bulik03   Chitin synthesis1455547111
Yoshimoto02_Na   Na(+) exposure1205803316
Gasch00_steadyState_y14   0
Sapra04   Pre-mRNA splicing factor mutants at restrictive temperature time course1545211424
Causton01_sorbitol   Sorbitol response111794186
Gasch00_HOtimeCourse   Hydrogen peroxide response time course111025219
Gasch00_HS29-33   Heat Shock 29C to 33C time course111025214
Segal03_HSkin82   Heat Shock, kin82 mutant1274057910
Gasch00_HS30-37   Heat Shock 30C to 37C time course111025215
Bro03   Lithium response127916857
Protchenko01   Iron concentration and AFT1 overexpression116734734
Jones03_orig   Ras/cAMP signal transduction pathway145709845
transfer_of_w.t._to_YPD   0
Gasch00_stationaryPhase_y12   0
Yamamoto05   Heat shock transcription factor 1 mutant response to heat stress156472834
Sudarsanam00_set2   Snf/Swi mutants (384_F_v1.0)107253598
Pramila06swap   0
Ferea99   Evolved strains104497614
Gasch00_carbonSources   Carbon sources111025216
Gasch00_Ndepletion   Nitrogen depletion time course111025219
Shapira04   oxidative stress responses1537154470
Bernstein00_TSA   Trichostatin A treatment time course110957435
Hardwick00   rapamycin exposure1061130414
Angus01   rsc3/rsc30 knockouts113366988
Gasch00_HSmild   Mild Heat Shock111025216

Contact: yguan@princeton.edu
Modified on Oct 06, 2009
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