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40643_2017_152_MOESM6_ESM.xlsx Additional file 6. Essential genes and partially essential genes predicted by iRY1078.

All genes involved in iYL_2.0 were classified into three categories: essential genes, partially essential genes, and non-essential genes.

The prediction of essential genes and partially essential genes was conducted using the singleGeneDeletion function based on Cobra Toolbox.

Fig. 2 The distributions of essential genes (in blue), partially essential genes (in red), and non-essential genes (in green) in cells grown in different media.

The singleGeneDeletion function in Cobra Toolbox v2.0 can be used to predict the essential genes, partially essential genes, and non-essential genes (Schellenberger et al. 2011).

Based on the simulated specific growth rate, the genes were classified into essential genes (the calculated specific growth rate was 0), partially essential genes (the calculated specific growth rate of P. pastoris was in the range from 0 to the maximum specific growth rate), and non-essential genes (the calculated specific growth rate was the same as the maximum specific growth rate).

The highest amount of partially-essential reactions was distributed in the central carbon metabolism.

Reactions which only caused growth retardation (partially-essential) accounted for 85 in iLC915 and 58 in iSS884 and iIN800.

Results have been distributed in three categories: essential, partially-essential, and non-essential (see materials and methods section).

Partially-essential reactions had Pmw values between of 0.01-to-0.99, hence a diminished growth rate was seen upon their deletion.

Four of those originate from the DTT time course, while the others are from transcription profiles of partially suppressed essential genes.