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Literature DB >> 21152265

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns.

Abstract

We present investigation of gene expression profiles by means of singular spectrum analysis (SSA). The biological problem under investigation is the decomposition of bicoid protein profiles of Drosophila melanogaster into the sum of a signal and noise, where the former consists of an exponential-in-distance pattern and is close to constant nonspecific component, or "background." The signal processing problems addressed are (i) trend extraction from a noisy signal, (ii) batch processing of similar data, and (iii) analytical approximation of the signal components by the sum of exponential and constant-like functions. The proposed methods are evaluated on the given 17 series.

Entities: Gene Species

Year: 2008 PMID： 21152265 PMCID： PMC2997757 DOI： 10.1155/2008/825758

Source DB: PubMed Journal: Res Lett Signal Process ISSN： 1687-6911

4 in total

1. A database for management of gene expression data in situ.

Authors: Ekaterina Poustelnikova; Andrei Pisarev; Maxim Blagov; Maria Samsonova; John Reinitz
Journal: Bioinformatics Date: 2004-04-01 Impact factor: 6.937

2. Removal of background signal from in situ data on the expression of segmentation genes in Drosophila.

Authors: Ekaterina Myasnikova; Maria Samsonova; David Kosman; John Reinitz
Journal: Dev Genes Evol Date: 2005-02-12 Impact factor: 0.900

3. Establishment of developmental precision and proportions in the early Drosophila embryo.

Authors: Bahram Houchmandzadeh; Eric Wieschaus; Stanislas Leibler
Journal: Nature Date: 2002-02-14 Impact factor: 49.962

4. Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products.

Authors: David M Holloway; Lionel G Harrison; David Kosman; Carlos E Vanario-Alonso; Alexander V Spirov
Journal: Dev Dyn Date: 2006-11 Impact factor: 3.780

4 in total

10 in total

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

Authors: Theodore Alexandrov; Nina Golyandina; David Holloway; Alex Shlemov; Alexander Spirov
Journal: J Comput Biol Date: 2018-08-17 Impact factor: 1.479

2. Formation of the bicoid morphogen gradient: an mRNA gradient dictates the protein gradient.

Authors: Alexander Spirov; Khalid Fahmy; Martina Schneider; Erich Frei; Markus Noll; Stefan Baumgartner
Journal: Development Date: 2009-02 Impact factor: 6.868

3. Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation.

Authors: David M Holloway; Francisco J P Lopes; Luciano da Fontoura Costa; Bruno A N Travençolo; Nina Golyandina; Konstantin Usevich; Alexander V Spirov
Journal: PLoS Comput Biol Date: 2011-02-03 Impact factor: 4.475

10. Cortical movement of Bicoid in early Drosophila embryos is actin- and microtubule-dependent and disagrees with the SDD diffusion model.

Authors: Xiaoli Cai; Mira Akber; Alexander Spirov; Stefan Baumgartner
Journal: PLoS One Date: 2017-10-03 Impact factor: 3.240

10 in total

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns.

1. A database for management of gene expression data in situ.

2. Removal of background signal from in situ data on the expression of segmentation genes in Drosophila.

3. Establishment of developmental precision and proportions in the early Drosophila embryo.

4. Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products.

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

2. Formation of the bicoid morphogen gradient: an mRNA gradient dictates the protein gradient.

3. Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation.

4. Bicoid signal extraction with a selection of parametric and nonparametric signal processing techniques.

5. Shaped 3D singular spectrum analysis for quantifying gene expression, with application to the early zebrafish embryo.

6. Spontaneous oscillation in cell adhesion and stiffness measured using atomic force microscopy.

7. Short-Term Forecasting of Daily Confirmed COVID-19 Cases in Malaysia Using RF-SSA Model.

8. Spatial bistability generates hunchback expression sharpness in the Drosophila embryo.

Review 9. A glance at the applications of Singular Spectrum Analysis in gene expression data.

10. Cortical movement of Bicoid in early Drosophila embryos is actin- and microtubule-dependent and disagrees with the SDD diffusion model.