A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data
<p>The Negative Binomial distribution (NBD) is used for modeling many types of count data, including gene expression counts obtained by RNA sequencing technologies (RNA-Seq). Finding outliers in this type of data has been shown in recent research to help in identifying rare genetic disorders i...
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| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | |
| منشور في: |
2021
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| الموضوعات: | |
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| _version_ | 1864513560296554496 |
|---|---|
| author | Edin Salkovic (16891479) |
| author2 | Halima Bensmail (10400) |
| author2_role | author |
| author_facet | Edin Salkovic (16891479) Halima Bensmail (10400) |
| author_role | author |
| dc.creator.none.fl_str_mv | Edin Salkovic (16891479) Halima Bensmail (10400) |
| dc.date.none.fl_str_mv | 2021-05-20T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1109/access.2021.3082311 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/A_Novel_Bayesian_Outlier_Score_Based_on_the_Negative_Binomial_Distribution_for_Detecting_Aberrantly_Expressed_Genes_in_RNA-Seq_Gene_Expression_Count_Data/24042444 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Genetics Information and computing sciences Data management and data science Mathematical sciences Statistics Data models Gene expression Bayes methods Computational modeling Anomaly detection Dispersion Sequential analysis Bayesian model Bayesian outlier score Gibbs sampling Mendelian disorder Negative binomial distribution Outlier detection Rare disease RNA-Seq |
| dc.title.none.fl_str_mv | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p>The Negative Binomial distribution (NBD) is used for modeling many types of count data, including gene expression counts obtained by RNA sequencing technologies (RNA-Seq). Finding outliers in this type of data has been shown in recent research to help in identifying rare genetic disorders in humans. Existing Bayesian approaches to detecting outliers in data following the NBD are either computationally inefficient or too general and hence do not leverage the NBD's specificities in an optimal way. We present a novel Bayesian outlier score for data following the NBD, relying on recent advances in the inference of its dispersion parameter through a special method of Gibbs sampling. The novel Bayesian model on which our score is based - OutPyRX (Outlier detection in Python for RNA-Seq, eXtended version) - improves the model of its predecessor OutPyR by introducing novel parameters that are derived from OutPyR's. These novel parameters allow more than 6 times faster convergence of the novel outlier score compared to OutPyR's while having a negligible computational impact on the Gibbs sampling procedure. We show that, in terms of area under precision-recall curve (AUC) values, the novel score outcompetes existing scores on 21 out of 24 datasets that we derived from 4 real datasets by injecting artificial outliers. However, OutPyRX does not perform confounder control which is required for some datasets containing biological outliers. The model is general and can be applied to other similar count data. The code for our model is available at <a href="https://github.com/esalkovic/outpyrx" rel="nofollow">https://github.com/esalkovic/outpyrx</a>.</p><h2>Other Information</h2><p>Published in: IEEE Access<br>License: <a href="https://creativecommons.org/licenses/by/4.0/legalcode" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1109/access.2021.3082311" target="_blank">https://dx.doi.org/10.1109/access.2021.3082311</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_a71ce69ccb88c94d6d1bfa0c4189d8dc |
| identifier_str_mv | 10.1109/access.2021.3082311 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/24042444 |
| publishDate | 2021 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count DataEdin Salkovic (16891479)Halima Bensmail (10400)Biological sciencesBioinformatics and computational biologyGeneticsInformation and computing sciencesData management and data scienceMathematical sciencesStatisticsData modelsGene expressionBayes methodsComputational modelingAnomaly detectionDispersionSequential analysisBayesian modelBayesian outlier scoreGibbs samplingMendelian disorderNegative binomial distributionOutlier detectionRare diseaseRNA-Seq<p>The Negative Binomial distribution (NBD) is used for modeling many types of count data, including gene expression counts obtained by RNA sequencing technologies (RNA-Seq). Finding outliers in this type of data has been shown in recent research to help in identifying rare genetic disorders in humans. Existing Bayesian approaches to detecting outliers in data following the NBD are either computationally inefficient or too general and hence do not leverage the NBD's specificities in an optimal way. We present a novel Bayesian outlier score for data following the NBD, relying on recent advances in the inference of its dispersion parameter through a special method of Gibbs sampling. The novel Bayesian model on which our score is based - OutPyRX (Outlier detection in Python for RNA-Seq, eXtended version) - improves the model of its predecessor OutPyR by introducing novel parameters that are derived from OutPyR's. These novel parameters allow more than 6 times faster convergence of the novel outlier score compared to OutPyR's while having a negligible computational impact on the Gibbs sampling procedure. We show that, in terms of area under precision-recall curve (AUC) values, the novel score outcompetes existing scores on 21 out of 24 datasets that we derived from 4 real datasets by injecting artificial outliers. However, OutPyRX does not perform confounder control which is required for some datasets containing biological outliers. The model is general and can be applied to other similar count data. The code for our model is available at <a href="https://github.com/esalkovic/outpyrx" rel="nofollow">https://github.com/esalkovic/outpyrx</a>.</p><h2>Other Information</h2><p>Published in: IEEE Access<br>License: <a href="https://creativecommons.org/licenses/by/4.0/legalcode" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1109/access.2021.3082311" target="_blank">https://dx.doi.org/10.1109/access.2021.3082311</a></p>2021-05-20T00:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1109/access.2021.3082311https://figshare.com/articles/journal_contribution/A_Novel_Bayesian_Outlier_Score_Based_on_the_Negative_Binomial_Distribution_for_Detecting_Aberrantly_Expressed_Genes_in_RNA-Seq_Gene_Expression_Count_Data/24042444CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/240424442021-05-20T00:00:00Z |
| spellingShingle | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data Edin Salkovic (16891479) Biological sciences Bioinformatics and computational biology Genetics Information and computing sciences Data management and data science Mathematical sciences Statistics Data models Gene expression Bayes methods Computational modeling Anomaly detection Dispersion Sequential analysis Bayesian model Bayesian outlier score Gibbs sampling Mendelian disorder Negative binomial distribution Outlier detection Rare disease RNA-Seq |
| status_str | publishedVersion |
| title | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| title_full | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| title_fullStr | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| title_full_unstemmed | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| title_short | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| title_sort | A Novel Bayesian Outlier Score Based on the Negative Binomial Distribution for Detecting Aberrantly Expressed Genes in RNA-Seq Gene Expression Count Data |
| topic | Biological sciences Bioinformatics and computational biology Genetics Information and computing sciences Data management and data science Mathematical sciences Statistics Data models Gene expression Bayes methods Computational modeling Anomaly detection Dispersion Sequential analysis Bayesian model Bayesian outlier score Gibbs sampling Mendelian disorder Negative binomial distribution Outlier detection Rare disease RNA-Seq |