Ste12: Ste12 knockout data under pheromone treatment versus wild...

Description Usage Format Details Author(s) References See Also Examples

Description

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.

Usage

1

Format

Ste12Data vector: 601 Ste12Beliefs matrix of example certainty: 42 x 2 Ste12Binding vector: 42

Details

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).

Author(s)

Ewa Szczurek

References

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.

See Also

miRNA,CellCycle

Examples

1
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4

Example output

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 

bgmm documentation built on Oct. 10, 2021, 5:07 p.m.