Data and information The regulatory network model MMH805/775, is combined with an existing genome-scale metabolic model, iND750 The relevant literature for each metabolic and transcription factor gene was collected through information in the SGD, YPD, and MiPS databases and direct pubmed searches
Data and information • The regulatory network model, iMH805/775, is combined with an existing genome-scale metabolic model, iND750. • The relevant literature for each metabolic and transcription factor gene was collected through information in the SGD, YPD, and MIPS databases and direct PubMed searches
Reconstructed transcriptional regulatory network Starting point: ND750 The regulatory network model part of MH805/775 consists of three layers which were implemented as Boolean rules derived from primary literature of MH805/775 The first layer: activities of 55 TFs in response to 67 extracellular and 15 intracellular metabolite concentrations The second layer: the rules describing the expression of 348 metabolic genes as a function of the transcription factor states and metabolite concentrations in cases in which the direct regulatory mechanisms were unknown. For the remaining metabolic genes, no information on regulation could be found in the literature, and they were assumed to be constitutively expressed in all environmental cond itions The third layer: the gene-protein -reaction associations that encode the relationship between gene expression and presence/absence of a particular reaction in the network
Reconstructed transcriptional regulatory network • Starting point: iND750 • The regulatory network model part of iMH805/775 consists of three layers which were implemented as Boolean rules derived from primary literature of iMH805/775. – The first layer: activities of 55 TFs in response to 67 extracellular and 15 intracellular metabolite concentrations. – The second layer: the rules describing the expression of 348 metabolic genes as a function of the transcription factor states and metabolite concentrations in cases in which the direct regulatory mechanisms were unknown. For the remaining metabolic genes, no information on regulation could be found in the literature, and they were assumed to be constitutively expressed in all environmental conditions. – The third layer: the gene–protein–reaction associations that encode the relationship between gene expression and presence/absence of a particular reaction in the network