ypd: In Sillico YPD Medium

Description

Apply in sillico medium to bakers yeast metabolic network model iND750 by Duarte et al. 2004.

Usage

ypd(model, def_bnd = SYBIL_SETTINGS("MAXIMUM"), ver = "harrison2007")

Arguments

model

An object of class modelorg.

def_bnd

A single numeric value. Absolute value for uppper and lower bounds for reaction bounds. Default: SYBIL_SETTINGS("MAXIMUM").

ver

A single character string giving the version of the YPD medium. Can be set to harrison2007 or bilu2006 (see Details below). Default: harrison2007.

Value

An instance of class modelorg with input fluxes set corresponding to the desired YPD medium.

encoding

utf8

Details

The function ypd identifies exchange reactions via the function findExchReact. The lower bounds of all exchange fluxes is set to zero (not allowing any flux into the network) and the upper bounds are set to the value of def_bnd (default: output is unbounded). The lower bound input of the input fluxes is set like in the table below. Two different versions of YPD medium are available: Harrison et al. 2007 and Bilu et al. 2006.

Harrison et al 2007: ll{ EX_ala_L(e) $-0.5$ EX_arg_L(e) $-0.5$ EX_asn_L(e) $-0.5$ EX_asp_L(e) $-0.5$ EX_chol(e) $-0.5$ EX_cys_L(e) $-0.5$ EX_dcyt(e) $-0.5$ EX_ergst(e) $-0.5$ EX_glc(e) $-20$ EX_glu_L(e) $-0.5$ EX_gly(e) $-0.5$ EX_gua(e) $-0.5$ EX_h(e) def_bnd * -1 EX_hdca(e) $-0.5$ EX_his_L(e) $-0.5$ EX_leu_L(e) $-0.5$ EX_lys_L(e) $-0.5$ EX_met_L(e) $-0.5$ EX_nh4(e) def_bnd * -1 EX_o2(e) $-2$ EX_ocdca(e) $-0.5$ EX_pi(e) def_bnd * -1 EX_pro_L(e) $-0.5$ EX_ser_L(e) $-0.5$ EX_so4(e) def_bnd * -1 EX_thr_L(e) $-0.5$ EX_thymd(e) $-0.5$ EX_trp_L(e) $-0.5$ EX_ttdca(e) $-0.5$ EX_tyr_L(e) $-0.5$ EX_ura(e) $-0.5$ }

Bilu et al 2006: ll{ EX_nh4(e) def_bnd * -1 EX_pi(e) def_bnd * -1 EX_so4(e) def_bnd * -1 EX_glc(e) $-20$ EX_o2(e) $-2$ EX_ala_L(e) $-0.5$ EX_arg_L(e) $-0.5$ EX_asn_L(e) $-0.5$ EX_asp_L(e) $-0.5$ EX_cys_L(e) $-0.5$ EX_his_L(e) $-0.5$ EX_leu_L(e) $-0.5$ EX_lys_L(e) $-0.5$ EX_met_L(e) $-0.5$ EX_pro_L(e) $-0.5$ EX_ser_L(e) $-0.5$ EX_thr_L(e) $-0.5$ EX_trp_L(e) $-0.5$ EX_tyr_L(e) $-0.5$ EX_dcyt(e) $-0.5$ EX_gly(e) $-0.5$ EX_gua(e) $-0.5$ EX_thymd(e) $-0.5$ EX_h2o(e) def_bnd * -1 EX_na1(e) def_bnd * -1 EX_k(e) def_bnd * -1 EX_co2(e) def_bnd * -1 EX_ade(e) $-0.5$ EX_gln_L(e) $-0.5$ EX_ile_L(e) $-0.5$ EX_phe_L(e) $-0.5$ EX_val_L(e) $-0.5$ }

References

Harrison, R., Papp, B., Pal, C., Oliver, S. G. and Delnert, D. (2007) Plasticity of genetic interactions in metabolic networks of yeast. PNAS 104, 2307--2312.

Bilu, Y., Shlomi, T., Barkai, N. and Ruppin, E. (2006) Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput Biol 2, 932--938.