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Shaped singular spectrum analysis for quantifying gene expression, with application to the early Drosophila embryo.

Shlemov A, Golyandina N, Holloway D, Spirov A - Biomed Res Int (2015)

Bottom Line: We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo.We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes.Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Mathematics and Mechanics, St. Petersburg State University, Universitetsky Pr. 28, Peterhof, St. Petersburg 198504, Russia.

ABSTRACT
In recent years, with the development of automated microscopy technologies, the volume and complexity of image data on gene expression have increased tremendously. The only way to analyze quantitatively and comprehensively such biological data is by developing and applying new sophisticated mathematical approaches. Here, we present extensions of 2D singular spectrum analysis (2D-SSA) for application to 2D and 3D datasets of embryo images. These extensions, circular and shaped 2D-SSA, are applied to gene expression in the nuclear layer just under the surface of the Drosophila (fruit fly) embryo. We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo. We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes. Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns.

No MeSH data available.


hb (a) and ftz (b): reconstruction from all striped components.
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fig7: hb (a) and ftz (b): reconstruction from all striped components.

Mentions: Figure 6 shows reconstructions from the leading high frequency components for each image, components 5 and 6 from Figure 4, components 2 and 3 from Figure 5. The reconstructions are very similar, but have opposite phases, indicating that the hb data was overcorrected. Figure 7 is reconstructed from all striped components for each image; again, the patterns are very similar but of opposite phase.


Shaped singular spectrum analysis for quantifying gene expression, with application to the early Drosophila embryo.

Shlemov A, Golyandina N, Holloway D, Spirov A - Biomed Res Int (2015)

hb (a) and ftz (b): reconstruction from all striped components.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402483&req=5

fig7: hb (a) and ftz (b): reconstruction from all striped components.
Mentions: Figure 6 shows reconstructions from the leading high frequency components for each image, components 5 and 6 from Figure 4, components 2 and 3 from Figure 5. The reconstructions are very similar, but have opposite phases, indicating that the hb data was overcorrected. Figure 7 is reconstructed from all striped components for each image; again, the patterns are very similar but of opposite phase.

Bottom Line: We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo.We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes.Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Mathematics and Mechanics, St. Petersburg State University, Universitetsky Pr. 28, Peterhof, St. Petersburg 198504, Russia.

ABSTRACT
In recent years, with the development of automated microscopy technologies, the volume and complexity of image data on gene expression have increased tremendously. The only way to analyze quantitatively and comprehensively such biological data is by developing and applying new sophisticated mathematical approaches. Here, we present extensions of 2D singular spectrum analysis (2D-SSA) for application to 2D and 3D datasets of embryo images. These extensions, circular and shaped 2D-SSA, are applied to gene expression in the nuclear layer just under the surface of the Drosophila (fruit fly) embryo. We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo. We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes. Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns.

No MeSH data available.