Year 2018, Volume 47 , Issue 5, Pages 1335 - 1347 2018-10-16

Overdispersed count models for mRNA transcription

Burcin Simsek [1] , Satish Iyengar [2]


Direct detection of gene activity is often not possible because new proteins from an individual activation event are masked by proteins remaining from previous events. Thus, researchers determine gene activation or inactivation by observing messenger RNA (mRNA) production instead. Typically, mRNA transcription occurs in short rapid bursts when the gene is in its on-state, and no transcriptions during its offstate. This burstiness of mRNA production is not well modeled by a Poisson process. We propose the Conway-Maxwell-Poisson (COM- Poisson) distribution as a potential alternative to the more common negative binomial (NB) distribution. We use the generalized linear model version of these models to incorporate covariate information. We also consider zero inflation to model excess zero counts. We use data from E. coli bacteria and mammalian cells to illustrate our proposed methods. We find that when there is a biophysically derived distribution, this distribution performs well. We also show that in the absence of such biophysical knowledge, the COM-Poisson is competitive with the NB. Both the COM-Poisson and NB arise in queueing theory, suggesting that further application of that framework to study mRNA dynamics would be useful.
Conway-Maxwell-Poisson, Link function, Model comparison, Negative binomial, Generalized linear model
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Primary Language en
Subjects Mathematics
Journal Section Statistics
Authors

Author: Burcin Simsek (Primary Author)
Institution: DEPARTMENT OF STATISTICS, UNIVERSITY OF PITTSBURGH
Country: United States


Author: Satish Iyengar
Institution: DEPARTMENT OF STATISTICS, UNIVERSITY OF PITTSBURGH
Country: United States


Dates

Publication Date : October 16, 2018

Bibtex @research article { hujms471515, journal = {Hacettepe Journal of Mathematics and Statistics}, issn = {2651-477X}, eissn = {2651-477X}, address = {}, publisher = {Hacettepe University}, year = {2018}, volume = {47}, pages = {1335 - 1347}, doi = {}, title = {Overdispersed count models for mRNA transcription}, key = {cite}, author = {Simsek, Burcin and Iyengar, Satish} }
APA Simsek, B , Iyengar, S . (2018). Overdispersed count models for mRNA transcription. Hacettepe Journal of Mathematics and Statistics , 47 (5) , 1335-1347 . Retrieved from https://dergipark.org.tr/en/pub/hujms/issue/39860/471515
MLA Simsek, B , Iyengar, S . "Overdispersed count models for mRNA transcription". Hacettepe Journal of Mathematics and Statistics 47 (2018 ): 1335-1347 <https://dergipark.org.tr/en/pub/hujms/issue/39860/471515>
Chicago Simsek, B , Iyengar, S . "Overdispersed count models for mRNA transcription". Hacettepe Journal of Mathematics and Statistics 47 (2018 ): 1335-1347
RIS TY - JOUR T1 - Overdispersed count models for mRNA transcription AU - Burcin Simsek , Satish Iyengar Y1 - 2018 PY - 2018 N1 - DO - T2 - Hacettepe Journal of Mathematics and Statistics JF - Journal JO - JOR SP - 1335 EP - 1347 VL - 47 IS - 5 SN - 2651-477X-2651-477X M3 - UR - Y2 - 2017 ER -
EndNote %0 Hacettepe Journal of Mathematics and Statistics Overdispersed count models for mRNA transcription %A Burcin Simsek , Satish Iyengar %T Overdispersed count models for mRNA transcription %D 2018 %J Hacettepe Journal of Mathematics and Statistics %P 2651-477X-2651-477X %V 47 %N 5 %R %U
ISNAD Simsek, Burcin , Iyengar, Satish . "Overdispersed count models for mRNA transcription". Hacettepe Journal of Mathematics and Statistics 47 / 5 (October 2018): 1335-1347 .
AMA Simsek B , Iyengar S . Overdispersed count models for mRNA transcription. Hacettepe Journal of Mathematics and Statistics. 2018; 47(5): 1335-1347.
Vancouver Simsek B , Iyengar S . Overdispersed count models for mRNA transcription. Hacettepe Journal of Mathematics and Statistics. 2018; 47(5): 1347-1335.