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Requires: PRO_FILE_NAME Column 1-4, NB_MOLECULES, EXPRESSION_K, EXPRESSION_X1 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
(1) y=(x x 0 ) k exp −(x x 1 )−(x x 1 ) 2
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]. |