Abstract:
:Recent progress in microscopy technologies, biological markers, and automated processing methods is making possible the development of gene expression atlases at cellular-level resolution over whole embryos. Raw data on gene expression is usually very noisy. This noise comes from both experimental (technical/methodological) and true biological sources (from stochastic biochemical processes). In addition, the cells or nuclei being imaged are irregularly arranged in 3D space. This makes the processing, extraction, and study of expression signals and intrinsic biological noise a serious challenge for 3D data, requiring new computational approaches. Here, we present a new approach for studying gene expression in nuclei located in a thick layer around a spherical surface. The method includes depth equalization on the sphere, flattening, interpolation to a regular grid, pattern extraction by Shaped 3D singular spectrum analysis (SSA), and interpolation back to original nuclear positions. The approach is demonstrated on several examples of gene expression in the zebrafish egg (a model system in vertebrate development). The method is tested on several different data geometries (e.g., nuclear positions) and different forms of gene expression patterns. Fully 3D datasets for developmental gene expression are becoming increasingly available; we discuss the prospects of applying 3D-SSA to data processing and analysis in this growing field.
journal_name
Biomed Res Intjournal_title
BioMed research internationalauthors
Shlemov A,Golyandina N,Holloway D,Spirov Adoi
10.1155/2015/986436subject
Has Abstractpub_date
2015-01-01 00:00:00pages
986436eissn
2314-6133issn
2314-6141journal_volume
2015pub_type
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/3892685
更新日期:2016-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/6701793
更新日期:2016-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 临床试验,杂志文章
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journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2020/5606573
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pub_type: 杂志文章,评审
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/7435054
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/549785
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journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2015/940278
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/2010453
更新日期:2019-10-07 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/106902
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 已发布勘误
doi:10.1155/2017/1641589
更新日期:2017-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/8526190
更新日期:2018-11-25 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/951081
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2013/101597
更新日期:2013-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/260210
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/853083
更新日期:2013-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/532792
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/382891
更新日期:2014-01-01 00:00:00
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pub_type: 杂志文章
doi:10.1155/2014/470253
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/214618
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/785474
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,随机对照试验
doi:10.1155/2014/646347
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2017/8017541
更新日期:2017-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/578698
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/2123787
更新日期:2020-05-20 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,随机对照试验
doi:10.1155/2016/6015761
更新日期:2016-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/934387
更新日期:2015-01-01 00:00:00