Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study
With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association b...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2008-01-01
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| Series: | Cancer Informatics |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=524 |
| _version_ | 1811339552209502208 |
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| author | Debashis Ghosh Hyungwon Choi Wenjuan Gu |
| author_facet | Debashis Ghosh Hyungwon Choi Wenjuan Gu |
| author_sort | Debashis Ghosh |
| collection | DOAJ |
| description | With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations. |
| first_indexed | 2024-04-13T18:28:23Z |
| format | Article |
| id | doaj.art-42fc21218ac146f6a6b66150e319676e |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-04-13T18:28:23Z |
| publishDate | 2008-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-42fc21218ac146f6a6b66150e319676e2022-12-22T02:35:11ZengSAGE PublishingCancer Informatics1176-93512008-01-0161723Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical StudyDebashis GhoshHyungwon ChoiWenjuan GuWith an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations.http://la-press.com/article.php?article_id=524circular binary segmentationhigh-dimensional datamachine learningtwo-color microarray platform |
| spellingShingle | Debashis Ghosh Hyungwon Choi Wenjuan Gu Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study Cancer Informatics circular binary segmentation high-dimensional data machine learning two-color microarray platform |
| title | Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study |
| title_full | Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study |
| title_fullStr | Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study |
| title_full_unstemmed | Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study |
| title_short | Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study |
| title_sort | global associations between copy number and transcript mrna microarray data an empirical study |
| topic | circular binary segmentation high-dimensional data machine learning two-color microarray platform |
| url | http://la-press.com/article.php?article_id=524 |
| work_keys_str_mv | AT debashisghosh globalassociationsbetweencopynumberandtranscriptmrnamicroarraydataanempiricalstudy AT hyungwonchoi globalassociationsbetweencopynumberandtranscriptmrnamicroarraydataanempiricalstudy AT wenjuangu globalassociationsbetweencopynumberandtranscriptmrnamicroarraydataanempiricalstudy |