Bayesian Correlation Analysis for Sequence Count Data.
Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. Th...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5049778?pdf=render |
| _version_ | 1811206357514190848 |
|---|---|
| author | Daniel Sánchez-Taltavull Parameswaran Ramachandran Nelson Lau Theodore J Perkins |
| author_facet | Daniel Sánchez-Taltavull Parameswaran Ramachandran Nelson Lau Theodore J Perkins |
| author_sort | Daniel Sánchez-Taltavull |
| collection | DOAJ |
| description | Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset. |
| first_indexed | 2024-04-12T03:46:06Z |
| format | Article |
| id | doaj.art-24019a6a3a564497b88e66d2efc34fb2 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T03:46:06Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-24019a6a3a564497b88e66d2efc34fb22022-12-22T03:49:08ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-011110e016359510.1371/journal.pone.0163595Bayesian Correlation Analysis for Sequence Count Data.Daniel Sánchez-TaltavullParameswaran RamachandranNelson LauTheodore J PerkinsEvaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.http://europepmc.org/articles/PMC5049778?pdf=render |
| spellingShingle | Daniel Sánchez-Taltavull Parameswaran Ramachandran Nelson Lau Theodore J Perkins Bayesian Correlation Analysis for Sequence Count Data. PLoS ONE |
| title | Bayesian Correlation Analysis for Sequence Count Data. |
| title_full | Bayesian Correlation Analysis for Sequence Count Data. |
| title_fullStr | Bayesian Correlation Analysis for Sequence Count Data. |
| title_full_unstemmed | Bayesian Correlation Analysis for Sequence Count Data. |
| title_short | Bayesian Correlation Analysis for Sequence Count Data. |
| title_sort | bayesian correlation analysis for sequence count data |
| url | http://europepmc.org/articles/PMC5049778?pdf=render |
| work_keys_str_mv | AT danielsancheztaltavull bayesiancorrelationanalysisforsequencecountdata AT parameswaranramachandran bayesiancorrelationanalysisforsequencecountdata AT nelsonlau bayesiancorrelationanalysisforsequencecountdata AT theodorejperkins bayesiancorrelationanalysisforsequencecountdata |