TY - JOUR

T1 - Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data

AU - Alexandrov, Theodore

AU - Golyandina, Nina

AU - Holloway, D.

AU - Shlemov, Alex

AU - Spirov, A.

PY - 2018/11/1

Y1 - 2018/11/1

N2 - Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information for the downstream segmentation genes, affecting the fly body plan. More recently, a number of researchers have focused on the patterning dynamics of the underlying bcd messenger RNA (mRNA) gradient, which is translated into Bcd protein. New, more accurate techniques for visualizing bcd mRNA need to be combined with quantitative signal extraction techniques to reconstruct the bcd mRNA distribution. Here, we present a robust technique for quantifying gradients with a two-exponential model. This approach (1) has natural, biologically relevant parameters and (2) is invariant to linear transformations of the data arising due to variation in experimental conditions (e.g., microscope settings, nonspecific background signal). This allows us to quantify bcd mRNA gradient variability from embryo to embryo (important for studying the robustness of developmental regulatory networks); sort out atypical gradients; and classify embryos to developmental stage by quantitative gradient parameters.

AB - Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information for the downstream segmentation genes, affecting the fly body plan. More recently, a number of researchers have focused on the patterning dynamics of the underlying bcd messenger RNA (mRNA) gradient, which is translated into Bcd protein. New, more accurate techniques for visualizing bcd mRNA need to be combined with quantitative signal extraction techniques to reconstruct the bcd mRNA distribution. Here, we present a robust technique for quantifying gradients with a two-exponential model. This approach (1) has natural, biologically relevant parameters and (2) is invariant to linear transformations of the data arising due to variation in experimental conditions (e.g., microscope settings, nonspecific background signal). This allows us to quantify bcd mRNA gradient variability from embryo to embryo (important for studying the robustness of developmental regulatory networks); sort out atypical gradients; and classify embryos to developmental stage by quantitative gradient parameters.

KW - Bicoid

KW - bcd mRNA gradient

KW - singular spectrum analysis

KW - spatial pattern

KW - two-exponential model

KW - DYNAMICS

KW - SIGNALS

KW - BICOID MESSENGER-RNA

KW - MORPHOGEN GRADIENT

KW - PRECISION

UR - http://www.scopus.com/inward/record.url?scp=85056321405&partnerID=8YFLogxK

UR - https://www.liebertpub.com/doi/10.1089/cmb.2017.0063

UR - http://www.mendeley.com/research/twoexponential-models-gene-expression-patterns-noisy-experimental-data

U2 - 10.1089/cmb.2017.0063

DO - 10.1089/cmb.2017.0063

M3 - Article

C2 - 30117746

VL - 25

SP - 1220

EP - 1230

JO - Journal of Computational Biology

JF - Journal of Computational Biology

SN - 1066-5277

IS - 11

ER -