omimIds              package:goProfiles              R Documentation

_E_n_t_r_e_z _i_d_e_n_t_i_f_i_e_r_s _f_o_r _d_i_s_e_a_s_e-_r_e_l_a_t_e_d _g_e_n_e_s _i_n _t_h_e _O_M_I_M _d_a_t_a_b_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

     Entrez identifiers for several lists of genes related with human
     disease. 

     '_d_i_s_e_a_s_e_I_d_s' contains the Entrez identifiers corresponding to
          disease-related genes found in the OMIM database. This list
          has been manually curated by Nuria Lopez-Bigas et al. who
          kindly provided it to us.

     '_m_o_r_b_i_d_m_a_p_I_d_s' contains the Entrez identifiers for all the genes
          in the morbidmap table. This list would correspond to
          disease-related genes if there had been no manual curation,
          as in the previous list ('diseaseIds').

     '_d_o_m_i_n_a_n_t_I_d_s' ontains the Entrez identifiers for dominant genes
          after manual curation by Nuria Lopez-Bigas who has kindly
          allowed us to include them in the package.

     '_r_e_c_e_s_s_i_v_e_I_d_s' contains the Entrez identifiers for recessive genes
          after manual curation by Nuria Lopez-Bigas who has kindly
          allowed us to include them in the package.

     '_d_o_m_i_n_a_n_t_I_d_s_E_B_I' contains the Entrez identifiers for dominant
          genes in the EBI version of the OMIM database recovered using
          SRS with the term 'dominant' in the KEYWORDS field.

     '_r_e_c_e_s_s_i_v_e_I_d_s_E_B_I' contains the Entrez identifiers for recessive
          genes in the EBI version of the OMIM database recovered using
          SRS with the term 'recessive' in the KEYWORDS field.

     '_d_o_m_i_n_a_n_t_I_d_s_N_C_B_I' contains the Entrez identifiers for dominant
          genes in the NCBI version of the OMIM database recovered
          using ENTREZ with the term 'dominant' in the CLINICAL field.

     '_r_e_c_e_s_s_i_v_e_I_d_s_N_C_B_I' contains the Entrez identifiers for recessive
          genes in the NCBI version of the OMIM database recovered
          using ENTREZ with the term 'recessive' in the CLINICAL field.

_U_s_a_g_e:

     data(omimIds)

_F_o_r_m_a_t:

     Each dataset is a character vector with a different number of
     elements which (should) correspond to valid Entrez identifiers

_D_e_t_a_i_l_s:

     Lopez-Bigas et al. analyzed the distribution of functional
     categories in genes causing disease in human. They did several
     comparisosn which can also be done using 'goProfiles'. In order to
     perform these comparisons we first tried to obtain the same lists
     of genes using standard database browsers, such as 'SRS', at the
     European Bioinformatics Institute, or 'Entrez', at the National
     Center for Biotechnological Information. Curiously both approaches
     provided very different lists so we asked the authors for their
     data and they kindly provided them to us. In order to facilitat
     the use of functions included in 'goProfiles' we have trimmed the
     list of recessive and dominant genes so that (i) They become
     exclussive (no gene belows to both lists) (2) They are both
     included in the 'diseaseIds' list. This eliminated 39 genes (out
     of 639) from the list of recessive genes and  52 genes (out of
     414) from the list of dominant genes

_R_e_f_e_r_e_n_c_e_s:

     Lopez-Bigas, N., Blencowe, B.J. and Ouzounis, C.A., Highly
     consistent patterns for inherited human diseases at the molecular
     level, Bioinformatics, 2006, 22 (3), 269-277.

_E_x_a_m_p_l_e_s:

     data(omimIds)

