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Parameter
Parameter Name | VariableDefault Value | Parameter Range | Description | |
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REF_FILE | file from which the reference annotation (GTF format) is read | |||
LOAD_CODING | true | {true,false} | flag to dis-/consider transcripts that have an annotated coding sequence | |
LOAD_NONCODING | true | {true,false} | flag to dis-/consider transcripts that are annotated to be non-coding | |
PRO_FILE | file to which the simulated expression values are written | |||
LIB_FILE | file to which the expressed transcript molecules are written | NB_MOLECULES
Overview
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EXPRESSION_K...
EXPRESSION_X0...
EXPRESSION_X1...
The Distribution of Gene Expression Levels
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In the beginning, the Flux Simulator reads the transcripts of the reference annotation and clusters genomic overlapping ones into loci.
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The "Gene Expression" step employs the annotation specified by REF_FILE_NAME and creates an artificial expression profile of the described transcripts. By the flag LOAD_CODING transcripts with an annotated coding sequence are taken into account, by LOAD_NONCODING correspondingly those which don't. Results from in silico gene expression are stored in the files specified by the parameters PRO_FILE respectively LIB_FILE; if no explicit values are provided for these parameters, then the corresponding files are created in the folder of the parameter file. |
Details
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where denotes the rank number of a gene and is the exponent of the intrinsic power law, and respectively control the exponential decay. The Flux Simulator assigns to the transcripts in the reference annotation randomly expression ranks which then are turned into relative expression levels by the modified Zipf's Law above, which determines the initial number of molecules by multiplication with the total numbers of molecules. Default values for parameters and have been estimated for mammalian cells by non-linear fitting to expression levels observed in experimental results. |
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Output: The first 6 columns of the PRO_FILE |
Transcript Modifications during Expression
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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]. |
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Overview
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