Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)
Abstract Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-10-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-022-04972-9 |
| _version_ | 1811194899050004480 |
|---|---|
| author | Yiru Sheng R. Ayesha Ali Andreas Heyland |
| author_facet | Yiru Sheng R. Ayesha Ali Andreas Heyland |
| author_sort | Yiru Sheng |
| collection | DOAJ |
| description | Abstract Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative dataset on transcriptional processes across organisms. Yet, due to technical differences between the studies (sequencing, experimental design, and analysis) extracting usable comparative information and conducting meta-analyses remains challenging. Results We introduce Comparative RNA-Seq Metadata Analysis Pipeline (CoRMAP), a meta-analysis tool to retrieve comparative gene expression data from any RNA-Seq dataset using de novo assembly, standardized gene expression tools and the implementation of OrthoMCL, a gene orthology search algorithm. It employs the use of orthogroup assignments to ensure the accurate comparison of gene expression levels between experiments and species. Here we demonstrate the use of CoRMAP on two mouse brain transcriptomes with similar scope, that were collected several years from each other using different sequencing technologies and analysis methods. We also compare the performance of CoRMAP with a functional mapping tool, previously published. Conclusion CoRMAP provides a framework for the meta-analysis of RNA-Seq data from divergent taxonomic groups. This method facilitates the retrieval and comparison of gene expression levels from published data sets using standardized assembly and analysis. CoRMAP does not rely on reference genomes and consequently facilitates direct comparison between diverse studies on a range of organisms. |
| first_indexed | 2024-04-12T00:35:01Z |
| format | Article |
| id | doaj.art-3a15001f5f9449139b049760555a01f0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T00:35:01Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3a15001f5f9449139b049760555a01f02022-12-22T03:55:11ZengBMCBMC Bioinformatics1471-21052022-10-0123111510.1186/s12859-022-04972-9Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)Yiru Sheng0R. Ayesha Ali1Andreas Heyland2Department of Mathematics and Statistics, University of GuelphDepartment of Mathematics and Statistics, University of GuelphIntegrative Biology, University of GuelphAbstract Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and at the single cell level. Collectively, this is a vast comparative dataset on transcriptional processes across organisms. Yet, due to technical differences between the studies (sequencing, experimental design, and analysis) extracting usable comparative information and conducting meta-analyses remains challenging. Results We introduce Comparative RNA-Seq Metadata Analysis Pipeline (CoRMAP), a meta-analysis tool to retrieve comparative gene expression data from any RNA-Seq dataset using de novo assembly, standardized gene expression tools and the implementation of OrthoMCL, a gene orthology search algorithm. It employs the use of orthogroup assignments to ensure the accurate comparison of gene expression levels between experiments and species. Here we demonstrate the use of CoRMAP on two mouse brain transcriptomes with similar scope, that were collected several years from each other using different sequencing technologies and analysis methods. We also compare the performance of CoRMAP with a functional mapping tool, previously published. Conclusion CoRMAP provides a framework for the meta-analysis of RNA-Seq data from divergent taxonomic groups. This method facilitates the retrieval and comparison of gene expression levels from published data sets using standardized assembly and analysis. CoRMAP does not rely on reference genomes and consequently facilitates direct comparison between diverse studies on a range of organisms.https://doi.org/10.1186/s12859-022-04972-9Gene expressionBrainRNA-SeqDiversity |
| spellingShingle | Yiru Sheng R. Ayesha Ali Andreas Heyland Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) BMC Bioinformatics Gene expression Brain RNA-Seq Diversity |
| title | Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) |
| title_full | Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) |
| title_fullStr | Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) |
| title_full_unstemmed | Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) |
| title_short | Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP) |
| title_sort | comparative transcriptomics analysis pipeline for the meta analysis of phylogenetically divergent datasets cormap |
| topic | Gene expression Brain RNA-Seq Diversity |
| url | https://doi.org/10.1186/s12859-022-04972-9 |
| work_keys_str_mv | AT yirusheng comparativetranscriptomicsanalysispipelineforthemetaanalysisofphylogeneticallydivergentdatasetscormap AT rayeshaali comparativetranscriptomicsanalysispipelineforthemetaanalysisofphylogeneticallydivergentdatasetscormap AT andreasheyland comparativetranscriptomicsanalysispipelineforthemetaanalysisofphylogeneticallydivergentdatasetscormap |