Mpact              package:yeastGSData              R Documentation

_P_r_o_t_e_i_n _I_n_t_e_r_a_c_t_i_o_n _D_a_t_a _f_r_o_m _M_p_a_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     The data are protein interactions, downloaded from MPACT. They are
     stored in a large character matrix, with seven columns, describing
     the interactions.

_U_s_a_g_e:

     data(Mpact)

_F_o_r_m_a_t:

     The data are stored as a matrix, with columns

   _O_R_F_1 The ORF for gene 1

   _G_E_N_E_1 The symbol for gene 1

   _O_R_F_2 The ORF for gene 2

   _G_E_N_E_2 The symbol for gene 2

   _D_E_S_C_R A description of one, or both genes

   _E_V_I An evidence code.

_D_e_t_a_i_l_s:

     It is unlikely that the variables 'GENE1' and 'GENE2' can be
     relied on, as names change, so 'ORF1' and 'ORF2' should be
     preferred, and even these should be compared to current databases
     to see if they have been  supplanted.

     The 'DESCR' field is incomplete, and seems to be inconsistent. It
     would probably better to rely on the the ORFs to obtain
     documentation on the ORFs from other sources.

     The 'EVI' variable, gives one, or more evidence codes, separate by
      commas ','.  The evidence codes are further detailed in the
     'MpactEvidenceCodes' data object.  Evidence codes can be helpful
     in filtering out interactions that might give rise to circularity
     in an analysis.  By that we mean, that if you are analyzing data
     that comes from one of the experiments that was used to establish
     this gold standard data set, it might be best to filter those
     interactions out. You should be careful to only filter them, if
     their only evidence is from the experiment  you are analyzing (if
     there is other evidence for the interaction it  should be
     retained).

_S_o_u_r_c_e:

     The data were downloaded from <URL:
     ftp://ftpmips.gsf.de/yeast/PPI/>.

_R_e_f_e_r_e_n_c_e_s:

     Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes
     HW, Stumpflen V(2006). MPact: the MIPS protein interaction
     resource on yeast. Nucl. Acids Res. 2006 34: D436-D441 PMID:
     16381906

_S_e_e _A_l_s_o:

     'MpactEvidenceCodes'

_E_x_a_m_p_l_e_s:

     data(Mpact)
     Mpact[1:3,]

