spYCCmeta              package:yeastCC              R Documentation

_m_e_t_a_d_a_t_a _o_n _y_e_a_s_t _c_e_l_l _c_y_c_l_e _m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     data.frame instance with metadata on 800 genes

_U_s_a_g_e:

     data(spYCCmeta)

_F_o_r_m_a_t:

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

     '_P_r_o_c_e_s_s' a factor with levels '' '4-nitroquinoline-N-oxide
          resistance' 'ATP synthesis' ...

     '_F_u_n_c_t_i_o_n' a factor with levels '' '(1->6)-beta-glucan synthase
          subunit' '(putative) Glc7p regulatory subunit' ...

     '_X' a logical vector

     '_P_e_a_k' a factor with levels 'G1' 'G2/M' 'M/G1' 'S' 'S/G2'

     '_P_h_a_s_e._O_r_d_e_r' a numeric vector

     '_C_l_u_s_t_e_r._O_r_d_e_r' a numeric vector

     '_O_R_F' a factor with levels '' 'YAL022C' 'YAL040C' 'YAL053W'
          'YAL067C' 'YAR003W' 'YAR007C'  ...

     '_Y_P_D' a factor with levels '' 'AAD10' 'ACE2' 'ADA2' 'ADK2' 'AFR1'
          'AGA1' 'AGA2' 'AGP1'  ...

     '_S_G_D' a factor with levels '' 'AAD10' 'ACE2' 'ADA2' 'ADK2' 'AFR1'
          'AGA1' 'AGA2' ...

     '_Y_P_D._1' a factor with levels '' 'YPD'

     '_S_G_D._1' a factor with levels '' 'SGD'

     '_M_I_P_S' a factor with levels '' 'MIPS'

     '_n_1' a numeric vector

     '_n_2' a numeric vector

     '_G_e_o_m_e_a_n' a numeric vector

     '_A_b_s_o_l_u_t_e' a numeric vector

     '_g_1' a numeric vector

     '_g_2' a numeric vector

     '_G_e_o_m_e_a_n._1' a numeric vector

     '_A_b_s_o_l_u_t_e._1' a numeric vector

     '_D_e_l_e_t_i_o_n' a factor with levels 'irrelevant' 'lethal'
          'undocumented' 'viable'

     '_K_n_o_w_n.' a factor with levels 'Known' 'New' 'New '

     '_D_e_s_c_r_i_p_t_i_o_n' 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 ' ...

     '_A_g_g_r_e_g_a_t_e._S_c_o_r_e' a numeric vector

     '_P_h_a_s_e' a numeric vector

     '_N_o.._E_l_e_m_e_n_t_s' a numeric vector

     '_M_o_s_t._R_e_l_e_v_a_n_t._P_r_o_m_o_t_e_r._E_l_e_m_e_n_t_s' 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'

     '_N_u_m_b_e_r' a numeric vector

     '_S_C_B' 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'  ...

     '_S_C_B._1' a factor with levels '' 'c178 tgaCACGAAAaac' 'c232
          gaaCACGAAAtgc' 'c539 gtaCACGAAAttc' 'w269 agcCACGAAAtgc'
          'w347 tgaCACGAAAtgt' 'w541 agtCACGAAAcgc' 'w601
          tgtCACGAAAagt'

     '_S_C_B._2' a factor with levels '' 'c330 aacCACGAAAaaa' 'c582
          agtCACGAAAcgc' 'w467 attCACGAAAtaa'

     '_S_C_B._3' a factor with levels '' 'w435 atcCACGAAAatc'

     '_X._8' a factor with levels '' 'w252 aacCACGAAAagt'

     '_N_u_m_b_e_r._1' a numeric vector

     '_S_C_B__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'  ....

     '_S_C_B__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'  ...

     '_S_C_B__d._2' a factor with levels '' 'c468 ccaCGCGAAAaga' 'c508
          tttCGCGAAAtct'

     '_S_C_B__d._3' a factor with levels '' 'c502 caaCGCGAAAaat'

     '_N_u_m_b_e_r._2' a numeric vector

     '_M_C_B' 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' ...

     '_M_C_B._1' a factor with levels '' 'w111 gaaACGCGTtct' 'w124
          ttgACGCGTttc' 'w128 gtgACGCGTtat' 'w130 agaACGCGTtct' 'w131
          gcgACGCGTaac' 'w138 aagACGCGTgaa' 'w139 attACGCGTtta' 'w153
          ctaACGCGTttt' ...

     '_M_C_B._2' a factor with levels '' 'w374 taaACGCGTcat'

     '_M_C_B._3' a factor with levels '' 'w309 aggACGCGTaaa'

     '_N_u_m_b_e_r._3' a numeric vector

     '_M_C_B__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' ...

     '_M_C_B__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' ...

     '_M_C_B__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' ...

     '_M_C_B__d._3' a factor with levels '' 'c 617 gaaACGCGcagta' 'w 50
          gtaACGCGctttt'

     '_X._9' a factor with levels '' 'c 359 acgACGCGccttc'

     '_N_u_m_b_e_r._4' a numeric vector

     '_S_F_F' a factor with levels ''
          'AATAGATGACCCGATTTGGAAAAAGGTAAACAACAATG'
          'ATTTGATTGCCGAAAGAGGCAAAAC  GTAAATAGGTTGT'
          'CAAAACAAACCCAATAAAGAAAATCCAAAATATAGAAC'
          'GTACTTTAACCTGTTTAGGAAAAAG  GTAAACAATAACA'
          'TCGAACAATTCTAAAAAGGTAAAT   AAAAACAATGGTA' ...

     '_N_u_m_b_e_r._5' a factor with levels '' '1' '2' '3' '4'
          'ATATAGCGACCGAATCAGGAAAAGGTCAACAACGAAG'

     '_S_w_i_5' 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' ...

     '_S_w_i_5._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' ...

     '_S_w_i_5._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' ...

     '_S_w_i_5._3' a factor with levels '' 'C 388 GGAACCAGCAGA' 'C 417
          TCGGCCAGCAAT' 'c 336 TTTACCAGCTCA' 'c 363 TGCACCAGCATT' 'c
          494 CTGGCCAGCAAG' 'w 396 GGAACCAGCAGA'

     '_N_u_m_b_e_r._6' a numeric vector

     '_S_w_i_5_e' 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' ...

     '_S_w_i_5_e._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'

     '_S_w_i_5_e._2' a factor with levels '' 'c 337 AGAGCCAGCAAG' 'c 417
          TCGGCCAGCAAT' 'c 642 GAGACCAGCGGA' 'w 447 AGAGCCAGCAAG'

     '_S_w_i_5_e._3' a factor with levels '' 'c 388 GGAACCAGCAGA' 'w 396
          GGAACCAGCAGA'

     '_N_u_m_b_e_r._7' a numeric vector

     '_E_C_B' 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'

     '_N_u_m_b_e_r._8' a numeric vector

     '_S_T_E_1_2' a factor with levels '' 'c 243
          CCTTTTTCAGTTTCTATTTTTAACACTGAAACT' 'w 112
          CCCTATTTGGTTGCAATTCAATTCCGTGAAACC' 'w 119
          CCCAATGTAGAAAAGTACATCATATGAAACA' 'w 218
          CCTAATTGGGTAAGTACATGATGAAACA' 'w 224
          CCCAAAAAGGAAATTTACATGTTAAATGAAACC' ...

     '_M_I_G_1._s_i_t_e_s' 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._1_0' a factor with levels '' 'c 161 AGTTTGGTGGGG' 'c 262
          AAGATGGTGGGG' 'c 498 AAAAAACCGGGG' 'c 499 AAAAATGCGGGG' 'w
          296 TATTCGGCGGGG' 'w 578 CTTTTGCCGGGG'

     '_X._1_1' a logical vector

_D_e_t_a_i_l_s:

     taken from the Spellman support web site.

_S_o_u_r_c_e:

     <URL: cellcycle-www.stanford.edu>

_R_e_f_e_r_e_n_c_e_s:

     PMID 9843569

_E_x_a_m_p_l_e_s:

     data(spYCCmeta)
     spYCCmeta[1:5,1:6]

