spYCCmeta {yeastCC}R Documentation

metadata on yeast cell cycle microarray experiment

Description

data.frame instance with metadata on 800 genes

Usage

data(spYCCmeta)

Format

A data frame with 800 observations on the following 75 variables.

Process
a factor with levels 4-nitroquinoline-N-oxide resistance ATP synthesis ...
Function
a factor with levels (1->6)-beta-glucan synthase subunit (putative) Glc7p regulatory subunit ...
X
a logical vector
Peak
a factor with levels G1 G2/M M/G1 S S/G2
Phase.Order
a numeric vector
Cluster.Order
a numeric vector
ORF
a factor with levels YAL022C YAL040C YAL053W YAL067C YAR003W YAR007C ...
YPD
a factor with levels AAD10 ACE2 ADA2 ADK2 AFR1 AGA1 AGA2 AGP1 ...
SGD
a factor with levels AAD10 ACE2 ADA2 ADK2 AFR1 AGA1 AGA2 ...
YPD.1
a factor with levels YPD
SGD.1
a factor with levels SGD
MIPS
a factor with levels MIPS
n1
a numeric vector
n2
a numeric vector
Geomean
a numeric vector
Absolute
a numeric vector
g1
a numeric vector
g2
a numeric vector
Geomean.1
a numeric vector
Absolute.1
a numeric vector
Deletion
a factor with levels irrelevant lethal undocumented viable
Known.
a factor with levels Known New New
Description
a factor with levels Inhibitor of Cdc28p/Cln1p and Cdc28p/Cln2p complexes involved in cell cycle arrest for mating 1,3-beta-D-glucan synthase 3\'-Phosphoadenylylsulfate reductase; part of the sulfate assimilation pathway ...
Aggregate.Score
a numeric vector
Phase
a numeric vector
No..Elements
a numeric vector
Most.Relevant.Promoter.Elements
a factor with levels AATAGATGACCCGATTTGGAAAAAGGTAAACAACAATG ATTTGATTGCCGAAAGAGGCAAAAC GTAAATAGGTTGT C 156 TCTGCCAGCCAA C 253 AAAGCCAGCCAT C 256 TATGCCAGCCAA C 276 AAGGCCAGCCTC C 293 TTGACCAGCTAA ...
X.1
a factor with levels ATATAGCGACCGAATCAGGAAAAG GTCAACAACGAAG C 102 CGAGCCAGCATT C 252 AAGACCAGCATG C 301 AGTGCCAGCAAA C 496 GAAGCCAGCACA C 550 GCGGCCAGCAAC c 106 attACGCGaaaat c 112 aaaACGCGagaaa c 121 ggaACGCGacgc ...
X.2
a factor with levels C 125 GCAACCAGCTCT C 146 CAAGCCAGCCAT C 195 CGCACCAGCAAC C 212 TATACCAGCGTT C 245 TAAACCAGCGCA C 402 TATGCCAGCAAA c 112 ttaACGCGatcga c 115 agtACGCGaaagg c 123 acaACGCGaacac c 127 gtgACGCGaaaaa ...
X.3
a factor with levels C 307 AAGACCAGCATT c 163 ctgACGCGcgaaa c 190 aatACGCGagaaa c 220 tagACGCGcctta c 241 cgaACGCGaaact c 275 aaaACGCGaccgt c 282 aagACGCGatttt c 289 attACGCGcatta c 290 aggACGCGaaact ...
X.4
a factor with levels C 200 CAAACCAGCATC c 117 gtcACGCGaaaaa c 314 cctACGCGaaagt c 338 caaACGCGaaaaa c 359 acgACGCGccttc c 382 gttACGCGaagtc c 384 tcaACGCGaattt c 397 aaaACGCGaaaac c 440 gtgACGCGcggtt ...
X.5
a factor with levels C 306 GGAGCCAGCGCG c 467 accACGCGaaaag c 588 gaaACGCGccaaa w 266 ATAACCAGCAAA w 383 cagACGCGagaac w 478 GGAGCCAGCGCG w401 tatCGCGAAAatt
X.6
a factor with levels C 337 AGAGCCAGCAAG C 417 TCGGCCAGCAAT c 501 acaACGCGaaaaa w 370 gcgACGCGaaaaa w 447 AGAGCCAGCAAG
X.7
a factor with levels C 388 GGAACCAGCAGA w 396 GGAACCAGCAGA
Number
a numeric vector
SCB
a factor with levels c 103 gacCACGAAAttt c 105 atgCACGAAAaag c 106 ctaCACGAAAcac c 108 tacCACGAAAgta c 110 ccaCACGAAAaga c 123 agaCACGAAAtgt c 127 acaCACGAAAacg c 181 cagCACGAAAtgg ...
SCB.1
a factor with levels c178 tgaCACGAAAaac c232 gaaCACGAAAtgc c539 gtaCACGAAAttc w269 agcCACGAAAtgc w347 tgaCACGAAAtgt w541 agtCACGAAAcgc w601 tgtCACGAAAagt
SCB.2
a factor with levels c330 aacCACGAAAaaa c582 agtCACGAAAcgc w467 attCACGAAAtaa
SCB.3
a factor with levels w435 atcCACGAAAatc
X.8
a factor with levels w252 aacCACGAAAagt
Number.1
a numeric vector
SCB_d
a factor with levels c 156 gatCGCGAAAttt c 184 cgaCGCGAAAatg c 218 cagCGCGAAAagt c 222 tatCGCGAAAaaa c 229 tgaCGCGAAAcgc c 237 tatCGCGAAAcga c 238 atcCGCGAAAgga c 283 aagCGCGAAAcaa ....
SCB_d.1
a factor with levels c 126 tttCGCGAAActg c 415 tttCGCGAAAtct c 566 ttcCGCGAAAaaa c 592 aggCGCGAAAtac c 633 aaaCGCGAAAtgt c242 gaaCGCGAAActt c297 ctcCGCGAAAaat c306 tcgCGCGAAAaga ...
SCB_d.2
a factor with levels c468 ccaCGCGAAAaga c508 tttCGCGAAAtct
SCB_d.3
a factor with levels c502 caaCGCGAAAaat
Number.2
a numeric vector
MCB
a factor with levels w 126 gcaACGCGTcgc w 187 caaACGCGTaca w 207 ctcACGCGTcgg w 209 attACGCGTtta w 226 cagACGCGTtgc w 228 acaACGCGTctt w 23 acaACGCGTgct w 267 cccACGCGTagg ...
MCB.1
a factor with levels w111 gaaACGCGTtct w124 ttgACGCGTttc w128 gtgACGCGTtat w130 agaACGCGTtct w131 gcgACGCGTaac w138 aagACGCGTgaa w139 attACGCGTtta w153 ctaACGCGTttt ...
MCB.2
a factor with levels w374 taaACGCGTcat
MCB.3
a factor with levels w309 aggACGCGTaaa
Number.3
a numeric vector
MCB_d
a factor with levels c 106 attACGCGaaaat c 109 acaACGCGactgg c 112 aaaACGCGagaaa c 115 agtACGCGaaagg c 117 gtcACGCGaaaaa c 121 ggaACGCGacgc c 127 gtgACGCGaaaaa c 129 acaACGCGcccga ...
MCB_d.1
a factor with levels c 123 acaACGCGaacac c 136 aatACGCGattgg c 147 gcaACGCGagaga c 158 tctACGCGcgaag c 163 ctgACGCGcgaaa c 176 gcgACGCGgttgt c 187 agtACGCGatttg c 189 gaaACGCGggcac ...
MCB_d.2
a factor with levels c 112 ttaACGCGatcga c 220 tagACGCGcctta c 294 ttcACGCGcttaa c 382 gttACGCGaagtc c 477 gcaACGCGcctgg c 501 acaACGCGaaaaa c 549 attACGCGcacg c 557 tgtACGCGcgaac ...
MCB_d.3
a factor with levels c 617 gaaACGCGcagta w 50 gtaACGCGctttt
X.9
a factor with levels c 359 acgACGCGccttc
Number.4
a numeric vector
SFF
a factor with levels AATAGATGACCCGATTTGGAAAAAGGTAAACAACAATG ATTTGATTGCCGAAAGAGGCAAAAC GTAAATAGGTTGT CAAAACAAACCCAATAAAGAAAATCCAAAATATAGAAC GTACTTTAACCTGTTTAGGAAAAAG GTAAACAATAACA TCGAACAATTCTAAAAAGGTAAAT AAAAACAATGGTA ...
Number.5
a factor with levels 1 2 3 4 ATATAGCGACCGAATCAGGAAAAGGTCAACAACGAAG
Swi5
a factor with levels C 102 CGAGCCAGCATT C 156 TCTGCCAGCCAA C 200 CAAACCAGCATC C 252 AAGACCAGCATG C 253 AAAGCCAGCCAT C 256 TATGCCAGCCAA C 276 AAGGCCAGCCTC C 293 TTGACCAGCTAA ...
Swi5.1
a factor with levels C 125 GCAACCAGCTCT C 146 CAAGCCAGCCAT C 195 CGCACCAGCAAC C 245 TAAACCAGCGCA C 301 AGTGCCAGCAAA C 306 GGAGCCAGCGCG C 307 AAGACCAGCATT C 402 TATGCCAGCAAA ...
Swi5.2
a factor with levels C 212 TATACCAGCGTT C 337 AGAGCCAGCAAG c 19 AGAACCAGCTGA c 320 ACCACCAGCTTA c 545 ACCACCAGCGTA c 569 TTCACCAGCGGC c 642 GAGACCAGCGGA c 651 ATCACCAGCAAA ...
Swi5.3
a factor with levels C 388 GGAACCAGCAGA C 417 TCGGCCAGCAAT c 336 TTTACCAGCTCA c 363 TGCACCAGCATT c 494 CTGGCCAGCAAG w 396 GGAACCAGCAGA
Number.6
a numeric vector
Swi5e
a factor with levels c 102 CGAGCCAGCATT c 137 TAGGCCAGCAAA c 155 ACAACCAGCAGT c 156 CTAACCAGCAAG c 16 AGAGCCAGCAGA c 174 TAAACCAGCATT c 184 ATGGCCAGCATA c 200 CAAACCAGCATC ...
Swi5e.1
a factor with levels c 222 TTGACCAGCGCC c 256 TAAACCAGCAAA c 306 GGAGCCAGCGCG c 307 AAGACCAGCATT c 637 GGAGCCAGCGAT w 265 TAAACCAGCAAT w 266 ATAACCAGCAAA w 467 TGAGCCAGCAAT w 478 GGAGCCAGCGCG w 536 GAAACCAGCAAC w 554 ATGGCCAGCACC
Swi5e.2
a factor with levels c 337 AGAGCCAGCAAG c 417 TCGGCCAGCAAT c 642 GAGACCAGCGGA w 447 AGAGCCAGCAAG
Swi5e.3
a factor with levels c 388 GGAACCAGCAGA w 396 GGAACCAGCAGA
Number.7
a numeric vector
ECB
a factor with levels c 185 TTACCCATTTAGGAAA c 221 TTACCCAATTAGGAAA c 251 TTTCCCTTTAAGGAAA c 258 TTTCCCAAAAAGGAAA c 387 TTTCCCTTTTAGGAAA c 394 TTACCCACTTAGGAAA w 154 TTTCCCTTTTAGGAAA w 177 TTACCCACTTAGGAAA w 229 TTACCCAGAAAGGAAA w 378 TTTCCCTAATAGGAAA w 453 TTTCCCGTTTAGGAAA w 595 TTTCCCACTAAGGAAA
Number.8
a numeric vector
STE12
a factor with levels c 243 CCTTTTTCAGTTTCTATTTTTAACACTGAAACT w 112 CCCTATTTGGTTGCAATTCAATTCCGTGAAACC w 119 CCCAATGTAGAAAAGTACATCATATGAAACA w 218 CCTAATTGGGTAAGTACATGATGAAACA w 224 CCCAAAAAGGAAATTTACATGTTAAATGAAACC ...
MIG1.sites
a factor with levels c 114 AATAGACTGGGG c 137 TCTATCCTGGGG c 147 TGAATGCTGGGG c 165 AATAAAGTGGGG c 215 TATAATGCGGGG c 304 AAATCGCCGGGG c 332 AAATATCTGGGG c 368 AATTGCGCGGGG ...
X.10
a factor with levels c 161 AGTTTGGTGGGG c 262 AAGATGGTGGGG c 498 AAAAAACCGGGG c 499 AAAAATGCGGGG w 296 TATTCGGCGGGG w 578 CTTTTGCCGGGG
X.11
a logical vector

Details

taken from the Spellman support web site.

Source

cellcycle-www.stanford.edu

References

PMID 9843569

Examples

data(spYCCmeta)
spYCCmeta[1:5,1:6]
[Package yeastCC version 1.2.8 Index]