Description Usage Format Details Author(s) References See Also Examples
Ste12 knockout expression data (Roberts et al., 2002) and knowledge from a Ste12 binding experiment (Harbison et al., 2004) used for identifying Ste12 target genes under pheromone treatment.
1 |
Ste12Data vector: 601 Ste12Beliefs matrix of example certainty: 42 x 2 Ste12Binding vector: 42
Ste12Data
Log2 expression ratios of Ste12 knockout versus
wild type, both under 50nM alpha-factor treatment for 30min. This
data is for 601 genes that had more than 1.5 fold change in expression
after pheromone treatment versus wild type.
Ste12Beliefs
: Gives the certainty (belief/plausibility) for
each out of 42 example Ste12 targets to belong to their cluster.
Ste12Beliefs
: Gives the certainty (belief/plausibility) for
each out of 42 example Ste12 targets to belong to their cluster. The
42 examples were chosen to meet two criteria: (1) Had a binding
p-value <0.0001 (see Ste12Binding
), and (2) Had a 2-fold change in response to pheromone treatment (versus wild-type)
Ste12Binding
: Gives the binding p-value for each example Ste12 target (see Ste12Belief
).
Ewa Szczurek
Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D., Dai, H., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. (2000). Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles. Science, 287(5454), 873–880.
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J.-B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., and Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99–104.
1 2 3 4 | data("Ste12")
print(Ste12Data)
print(Ste12Beliefs)
print(Ste12Binding)
|
Loading required package: mvtnorm
Loading required package: car
Loading required package: carData
Loading required package: lattice
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
YAL001C YAR007C YAR008W YAR040C YAR061W YBL002W YBL003C
0.7972627 0.5647278 1.0962363 0.8969206 -4.1191908 2.3917882 2.4250075
YBL009W YBL031W YBL035C YBL069W YBL070C YBL082C YBL083C
0.9301399 0.9301399 1.0630170 0.3321928 0.4982892 0.5647278 0.6311663
YBL086C YBR007C YBR009C YBR010W YBR054W YBR070C YBR071W
0.8637013 0.8637013 2.9897353 2.7239810 0.9633591 1.2623327 1.0630170
YBR073W YBR088C YBR089W YBR091C YBR093C YBR098W YBR124W
1.3287712 1.6277448 1.7938412 0.7972627 0.7308242 0.3986314 0.4982892
YBR243C YBR275C YCL014W YCL022C YCL023C YCL024W YCL060C
0.5647278 0.8969206 0.5315085 1.3287712 0.8969206 0.8637013 0.7640435
YCL061C YCL062W YCL063W YCL064C YCL069W YCLX09W YCR021C
0.2325350 0.5647278 0.3654121 0.9633591 0.5315085 1.2291134 1.1626748
YCR065W YDL003W YDL009C YDL011C YDL039C YDL048C YDL093W
0.4650699 2.2921304 0.8304820 0.4982892 0.5647278 1.0297977 0.5979471
YDL101C YDL163W YDL197C YDR016C YDR033W YDR082W YDR089W
1.3619905 0.4318507 0.8304820 0.7972627 0.6976049 0.7640435 0.7640435
YDR097C YDR113C YDR146C YDR176W YDR224C YDR225W YDR243C
0.9633591 1.1294556 0.6311663 0.9965784 2.6575425 2.6907618 1.0630170
YDR244W YDR269C YDR281C YDR297W YDR355C YDR380W YDR386W
1.1294556 0.2989735 0.7308242 0.8304820 0.6976049 1.3287712 0.8637013
YDR399W YDR403W YDR451C YDR481C YDR488C YEL016C YEL017W
0.8637013 0.5647278 1.5613062 0.9965784 0.7640435 0.8304820 0.6976049
YEL061C YEL065W YER001W YER003C YER032W YER053C YER054C
1.3287712 0.8969206 2.1260340 0.9965784 0.9965784 0.4318507 4.1191908
YER070W YER145C YER170W YFL014W YFL061W YFR026C YFR027W
2.6243232 1.0962363 0.7972627 0.8637013 0.5647278 0.6643856 0.6976049
YGL012W YGL032C YGL038C YGL093W YGL101W YGL138C YGL158W
0.6311663 0.3654121 0.9965784 1.3952098 0.5315085 2.2921304 0.9301399
YGL179C YGL217C YGR014W YGR108W YGR109C YGR138C YGR140W
1.2291134 0.2657542 0.7308242 0.9965784 1.2623327 1.3619905 0.6311663
YGR151C YGR152C YGR153W YGR176W YGR221C YHR031C YHR053C
1.0297977 0.9965784 0.8304820 0.4982892 1.4948676 0.6976049 0.7640435
YHR127W YHR136C YHR137W YHR146W YHR149C YHR153C YHR154W
0.8969206 1.1626748 1.0630170 0.3654121 0.9301399 1.2955520 2.0595954
YHR158C YHR172W YHR173C YHR215W YIL015W YIL016W YIL019W
0.6643856 0.7972627 1.4284291 0.8304820 1.1958941 1.0630170 0.5647278
YIL050W YIL066C YIL131C YIL132C YIL140W YIL141W YIL144W
0.6643856 0.7972627 0.5979471 0.6311663 1.4284291 1.0962363 0.6311663
YIR010W YJL019W YJL074C YJL091C YJL092W YJL115W YJL118W
0.7972627 1.0630170 1.2623327 0.8304820 1.8934990 0.9301399 1.1626748
YJL119C YJL120W YJL158C YJL181W YJL187C YJL196C YJL201W
1.0297977 0.6643856 0.8969206 0.8969206 1.2623327 0.8637013 0.5647278
YJL213W YJR009C YJR043C YJR048W YJR053W YJR060W YJR092W
0.5315085 0.7640435 0.5647278 0.7308242 0.8304820 0.5647278 0.6643856
YJR098C YJR128W YKL029C YKL030W YKL045W YKL049C YKL089W
0.6976049 0.3986314 0.9633591 0.7640435 1.2623327 0.7972627 0.9633591
YKL101W YKL113C YKL165C YKR010C YKR037C YKR077W YLL002W
1.6277448 1.2623327 0.5315085 0.7308242 1.3619905 1.2291134 1.1958941
YLL012W YLL021W YLL022C YLR045C YLR056W YLR103C YLR108C
0.5647278 0.7640435 0.8637013 1.3287712 1.0630170 1.0962363 0.9633591
YLR142W YLR183C YLR212C YLR233C YLR234W YLR235C YLR304C
1.9599376 2.3917882 0.8304820 0.8969206 1.2623327 0.9301399 5.9462513
YLR313C YLR326W YLR342W YLR348C YLR349W YLR373C YLR377C
1.2955520 0.8969206 0.6976049 1.0962363 0.8637013 0.6643856 0.6643856
YLR381W YLR424W YLR436C YML027W YML060W YML061C YML083C
0.7640435 0.5315085 0.6311663 2.1924725 0.7972627 1.2291134 0.7972627
YML085C YML102W YML123C YMR001C YMR003W YMR006C YMR048W
0.6311663 0.6976049 1.1626748 0.7308242 1.3619905 0.8969206 0.6643856
YMR069W YMR076C YMR078C YMR094W YMR096W YMR102C YMR117C
0.4982892 0.5979471 1.2955520 0.5315085 0.6311663 0.6976049 0.4982892
YMR144W YMR158W-A YMR179W YMR195W YMR199W YMR213W YMR215W
1.1294556 -0.1993157 1.2623327 0.9965784 2.3253497 0.5647278 1.3287712
YMR233W YMR274C YMR307W YMR319C YNL030W YNL031C YNL065W
0.7972627 0.6311663 1.1626748 0.6976049 1.7938412 2.4582268 0.7640435
YNL072W YNL082W YNL088W YNL102W YNL126W YNL160W YNL166C
1.2955520 0.6976049 0.7640435 1.3619905 1.6277448 1.2291134 1.0630170
YNL188W YNL197C YNL225C YNL231C YNL233W YNL262W YNL273W
1.0630170 0.4982892 0.7972627 1.1294556 0.6643856 0.6976049 0.5979471
YNL278W YNL304W YNL309W YNL312W YNR009W YNR045W YOL007C
0.6643856 0.5647278 0.8304820 0.9965784 1.3619905 1.0630170 1.6941833
YOL012C YOL017W YOL109W YOL113W YOR025W YOR026W YOR033C
1.0297977 1.7606219 0.8969206 1.0297977 0.6976049 0.7972627 0.8969206
YOR073W YOR074C YOR083W YOR084W YOR114W YOR144C YOR191W
1.1294556 1.8602797 0.8304820 0.6976049 0.7640435 0.6643856 0.4982892
YOR205C YOR237W YOR314W YOR372C YOR373W YOR379C YOR382W
6.2452248 0.8304820 0.5647278 0.5315085 1.4616484 0.3321928 0.9633591
YOR383C YPL014W YPL017C YPL018W YPL019C YPL045W YPL062W
0.7308242 1.5613062 1.2955520 0.9633591 0.7640435 5.8798127 1.2955520
YPL074W YPL082C YPL116W YPL124W YPL127C YPL153C YPL155C
0.6976049 0.5979471 0.3986314 1.3619905 1.8934990 1.1958941 0.3986314
YPL163C YPL164C YPL221W YPL255W YPL256C YPL267W YPL274W
2.0928147 0.8637013 0.3986314 0.9965784 1.7606219 1.7606219 5.8798127
YPR018W YPR031W YPR120C YPR124W YPR139C YPR149W YPR156C
0.7972627 0.7972627 1.5945255 0.6643856 0.5979471 0.8637013 0.7308242
YPR175W YPR203W NORF24 YAL028W YAL039C YAL040C YAL063C
0.7308242 0.1328771 -0.5315085 -0.7308242 -0.9965784 -1.1958941 -0.5647278
YAR009C YAR010C YAR031W YAR033W YAR068W YAR069C YBL005W-A
-0.6976049 -0.7308242 -1.5945255 -0.7972627 -1.1294556 -0.9301399 -0.7972627
YBL005W-B YBL016W YBL017C YBL101W-A YBL101W-B YBR012C YBR012W-A
-0.8304820 -2.3253497 -0.6976049 -1.3619905 -0.9965784 -0.8969206 -0.9965784
YBR012W-B YBR023C YBR032W YBR040W YBR056W YBR083W YBR143C
-0.3986314 -0.7640435 -6.3781019 -6.5441983 -0.3321928 -1.2291134 -0.9633591
YBR156C YBR158W YBR162C YBR183W YBR223C YBR224W YBR225W
-0.6643856 -1.3287712 -0.7972627 -0.8969206 -1.7606219 -1.3287712 -1.3619905
YBR226C YBR297W YCL018W YCL019W YCL020W YCL027W YCL055W
-1.8270605 -1.0297977 -0.8304820 -0.9965784 -1.2955520 -3.0229546 -2.7572003
YCL074W YCL075W YCL076W YCLX03C YCLX07W YCR009C YCR010C
-2.4250075 -6.4445405 -3.9530944 -0.6643856 -3.0229546 -1.7606219 -1.3952098
YCR089W YCR090C YCRX18C YDL022W YDL023C YDL026W YDL042C
-4.5842608 -1.0962363 -4.8500150 -1.0630170 -1.3619905 -0.6643856 -1.2291134
YDL127W YDL133W YDL135C YDL239C YDL240W YDR085C YDR107C
-2.3917882 -0.4982892 -1.3287712 -0.7308242 -0.6311663 -3.7205595 -1.5613062
YDR123C YDR124W YDR125C YDR241W YDR249C YDR250C YDR251W
-0.7640435 -4.0195330 -3.0561738 -1.6277448 -1.2291134 -1.1626748 -0.9633591
YDR277C YDR278C YDR309C YDR311W YDR330W YDR340W YDR366C
-0.7972627 -0.6311663 -1.4616484 -1.1626748 -0.5647278 -1.0962363 -0.9965784
YDR383C YDR385W YDR410C YDR461W YDR480W YDR490C YDR525W
-0.6976049 -0.7640435 -0.5315085 -1.0962363 -0.8304820 -6.4777598 -2.2256918
YDR530C YEL058W YER018C YER019C-A YER019W YER066C-A YER067W
-0.6643856 -0.6643856 -0.8969206 -0.2989735 -1.3619905 -0.8304820 -0.8304820
YER074W YER091C YER124C YER138C YER144C YER160C YER185W
-1.1958941 -1.2623327 -0.6976049 -0.4650699 -5.2154271 -0.4982892 -1.1294556
YER187W YER188W YFL011W YFL025C YFL026W YFL027C YFL039C
-1.9267183 -0.8637013 -0.6643856 -0.7308242 -1.5280869 -1.0630170 -0.6311663
YFL052W YFR015C YFR030W YFR053C YGL028C YGL033W YGL036W
-0.6976049 -0.5647278 -0.5647278 -0.9965784 -1.0962363 -0.7972627 -0.5647278
YGL051W YGL052W YGL053W YGL106W YGL118C YGL177W YGL184C
-0.7640435 -2.0263761 -2.8236389 -0.8304820 -1.1294556 -1.0297977 -0.7308242
YGL192W YGL193C YGL194C YGL205W YGL223C YGL253W YGR092W
-2.9232967 -1.6277448 -1.0962363 -5.1157693 -0.5979471 -0.5647278 -0.5315085
YGR122W YGR198W YGR232W YGR233C YGR243W YGR244C YHL022C
-0.8304820 0.0000000 -0.6311663 -0.8304820 -0.6976049 -0.5315085 -0.6643856
YHR005C YHR018C YHR030C YHR084W YHR097C YHR113W YHR124W
-0.9301399 -1.1294556 -0.4650699 -0.7640435 -0.8637013 -0.7640435 -0.6976049
YHR130C YHR142W YHR145C YHR151C YHR152W YHR205W YHR214C-B
-0.9301399 -0.5647278 -0.9633591 -0.4982892 -1.0630170 -1.4284291 -0.7972627
YHR214W YIL015C-A YIL037C YIL055C YIL060W YIL079C YIL080W
-0.8304820 -1.3287712 -6.4777598 -0.4318507 -0.9301399 -1.0962363 -3.9863137
YIL082W YIL082W-A YIL083C YIL117C YIL169C YIL170W YIL171W
-5.0161114 -2.5911039 -1.5945255 -1.1958941 -1.2291134 -0.9965784 -1.1958941
YIR037W YJL089W YJL107C YJL108C YJL113W YJL114W YJL157C
-0.3986314 -0.6311663 -2.5246654 -2.0928147 -1.0297977 -1.3287712 -2.0595954
YJL162C YJL163C YJL170C YJL218W YJL219W YJL220W YJR010W
-0.8637013 -1.0630170 -5.3150850 -1.7606219 -1.3287712 -0.7640435 -0.6311663
YJR026W YJR028W YJR029W YJR095W YJR111C YJR153W YKL102C
-1.0962363 -0.8969206 -0.6643856 -0.6643856 -0.5979471 -2.6907618 -0.6976049
YKL104C YKL127W YKL128C YKL189W YKL209C YKL221W YKR032W
-1.9599376 -1.3952098 -2.9897353 -2.2921304 -0.6643856 -2.5911039 -0.3986314
YKR033C YKR061W YKR098C YLL061W YLL062C YLR042C YLR120C
-0.6311663 -0.6976049 -0.7972627 -0.6311663 -0.7308242 -0.9633591 -0.9633591
YLR228C YLR241W YLR250W YLR267W YLR270W YLR273C YLR274W
-7.7400925 -0.4318507 -0.8969206 -0.4982892 -0.8637013 -0.4650699 -0.7972627
YLR286C YLR308W YLR327C YLR331C YLR332W YLR334C YLR343W
-0.5647278 -0.6643856 -0.6311663 -1.4616484 -1.3619905 -1.1958941 -0.6976049
YLR345W YLR416C YLR445W YLR452C YLR454W YML039W YML040W
-0.5315085 -0.8969206 -3.9198752 -1.9267183 -0.6311663 -0.4982892 -0.9633591
YML045W YML046W YML047C YML048W-A YML102C-A YML110C YMR011W
-0.5979471 -1.2623327 -5.0493307 -4.2188487 -4.1524101 -0.8637013 -0.9965784
YMR031W-A YMR045C YMR046C YMR051C YMR065W YMR173W YMR173W-A
-8.6037938 -0.5647278 -0.8969206 -0.8969206 -2.7904196 -0.5979471 -0.6643856
YMR196W YMR198W YMR232W YMR284W YMR304C-A YMR305C YMR315W
-0.5647278 -3.7205595 -3.6209016 -0.5647278 -1.7274026 -1.9599376 -0.9301399
YNL019C YNL033W YNL042W YNL045W YNL053W YNL058C YNL078W
-1.0297977 -1.1958941 -2.0595954 -0.5647278 -1.7606219 -0.6976049 -0.4982892
YNL092W YNL104C YNL105W YNL106C YNL145W YNL157W YNL192W
-1.0630170 -0.7640435 -1.7274026 -1.7938412 -1.2955520 -7.4411189 -1.4284291
YNL203C YNL208W YNL241C YNL272C YNL279W YNL280C YNL283C
-0.9965784 -1.6277448 -0.6976049 -0.6643856 -4.7835765 -1.3952098 -0.8969206
YNR044W YNR059W YOL006C YOL015W YOL083W YOL095C YOL104C
-4.2188487 -0.4318507 -6.6438562 -6.3116634 -0.2989735 -1.1958941 -0.9633591
YOL106W YOL118C YOL155C YOL156W YOL164W YOL166C YOR031W
-1.0630170 -0.3986314 -1.2291134 -1.3287712 -0.5647278 -2.3917882 -6.6106369
YOR045W YOR095C YOR126C YOR129C YOR130C YOR134W YOR220W
-7.0092683 -0.7308242 -0.5647278 -1.7938412 -1.8602797 -0.7640435 -0.5315085
YOR229W YOR285W YOR300W YOR337W YOR342C YOR343C YOR347C
-0.7308242 -0.5315085 -7.8065310 -1.3287712 -0.8969206 -2.9232967 -1.0630170
YOR355W YOR374W YPL058C YPL088W YPL119C YPL121C YPL131W
-0.8637013 -0.7972627 -0.7972627 -0.8637013 -1.0962363 -0.5315085 -0.5979471
YPL156C YPL177C YPL191C YPL192C YPL193W YPR039W YPR078C
-2.3253497 -0.7640435 -0.7308242 -4.7171379 -0.8304820 -0.7972627 -0.5315085
YPR087W YPR122W YPR140W YPR141C YPR158W YPR160W YPR165W
-0.5647278 -1.1626748 -1.1958941 -2.5246654 -0.6643856 -0.3986314 -0.4650699
1 2
YAL039C 0.6299502 0.37004976
YBR040W 0.8216358 0.17836417
YBR158W 0.7022776 0.29772236
YCL027W 0.9336100 0.06639004
YCL055W 0.8132194 0.18678064
YCR089W 0.9500000 0.05000000
YDL127W 0.8094774 0.19052260
YDL135C 0.7331109 0.26688909
YDR309C 0.7948042 0.20519577
YDR461W 0.6187579 0.38124213
YFL026W 0.8005371 0.19946288
YGL028C 0.7041558 0.29584425
YHR152W 0.5155385 0.48446150
YHR205W 0.8146079 0.18539207
YIL015C-A 0.5259870 0.47401299
YIL037C 0.8809525 0.11904749
YIL082W 0.8034736 0.19652641
YIL083C 0.8034736 0.19652641
YJL157C 0.8219055 0.17809449
YJL170C 0.7754849 0.22451510
YKL189W 0.8533617 0.14663833
YLR332W 0.6138661 0.38613390
YLR452C 0.6884958 0.31150421
YML046W 0.8078065 0.19219345
YML047C 0.8078065 0.19219345
YMR065W 0.6731155 0.32688451
YMR198W 0.8557611 0.14423890
YMR232W 0.6575212 0.34247883
YMR304C-A 0.7594342 0.24056576
YMR305C 0.7594342 0.24056576
YNL053W 0.6013757 0.39862430
YNL106C 0.6521856 0.34781441
YNL145W 0.8610985 0.13890153
YNL192W 0.8575695 0.14243051
YNL208W 0.6586356 0.34136438
YNL279W 0.9424089 0.05759109
YNL280C 0.9424089 0.05759109
YOR129C 0.8575695 0.14243051
YOR130C 0.5834600 0.41654000
YOR343C 0.8273183 0.17268168
YPL156C 0.8276196 0.17238036
YPL192C 0.7821419 0.21785806
YAL039C YBR040W YBR158W YCL027W YCL055W YCR089W YDL127W YDL135C
7.97e-06 1.91e-07 1.95e-06 2.16e-08 2.25e-07 1.57e-08 2.42e-07 1.07e-06
YDR309C YDR461W YFL026W YGL028C YHR152W YHR205W YIL015C-A YIL037C
3.22e-07 9.91e-06 2.88e-07 1.88e-06 7.39e-05 2.19e-07 6.03e-05 6.02e-08
YIL082W YIL083C YJL157C YJL170C YKL189W YLR332W YLR452C YML046W
2.72e-07 2.72e-07 1.90e-07 4.69e-07 1.03e-07 1.09e-05 2.55e-06 2.50e-07
YML047C YMR065W YMR198W YMR232W YMR304C-A YMR305C YNL053W YNL106C
2.50e-07 3.44e-06 9.83e-08 4.66e-06 6.41e-07 6.41e-07 1.39e-05 5.17e-06
YNL145W YNL192W YNL208W YNL279W YNL280C YOR129C YOR130C YOR343C
8.86e-08 9.49e-08 4.56e-06 1.82e-08 1.82e-08 9.49e-08 1.97e-05 1.71e-07
YPL156C YPL192C
1.70e-07 4.12e-07
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.