3.1 - Gene Expression

The cell group of the experiment is assigned a random expression profile where not necessarily all transcripts of the reference are expressed. Expression levels y   are connected with the relative expression rank x by a mixed power exponential law of the general form

where denotes the rank number of a gene,  the expression level of the highest abundant gene, and is the exponent of the underlying power law, and respectively  control the exponential decay. The Flux Simulator assigns to the transcripts in the reference annotation randomly expression ranks .

Subsequently, these ranks are turned into numbers of virtual molecules by the modified Zipf's Law above. Usually, p

art of the transcripts from the reference annotation will remains unexpressed.

After the number of RNA molecules has been determined for each transcript, in silico expressed transcripts are assigned individual variations in transcription start and the length of the attached poly-A tail. The FLUX SIMULATOR modeles differences in transcription start are modelled by random variables under an exponential model with a mean around 10nt. During poly-adenylation in the nucleus usually 200-250 adenine residues get added to the primary transcript. Disregarding other poly-adenylation mechanisms, as cytoplasmatic polyadenylation, and the exact mechanisms of degrading processes by exo- and endonucleases, our model describes poly-A lengths by randomly sampling under a Gaussian distribution with a mean of 125nt and shape adapted s.t. >99.5% of the random variables fall in the interval [0;250].