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Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis

Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li
2013 BMC Bioinformatics  
In our study, we used the MAQC data sets for systematically accessing the intra-and inter-platform concordance of GO terms enriched by Gene Set Enrichment Analysis (GSEA) and LRpath.  ...  Gene Ontology (GO) terms and pathways, and are widely used in genome-wide research.  ...  In our current study, we systematically investigated the intra-and inter-platform concordance of GO terms enriched by GSEA and LRpath.  ... 
doi:10.1186/1471-2105-14-143 pmid:23627640 pmcid:PMC3644270 fatcat:tlxl52b2wrbztcbdisynjo5ili

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

Seraya Maouche, Odette Poirier, Tiphaine Godefroy, Robert Olaso, Ivo Gut, Jean-Phillipe Collet, Gilles Montalescot, François Cambien
2008 BMC Genomics  
Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant  ...  Conclusion: Functional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference  ...  This work has been supported by a fellowship from Fondation pour la Recherche Medicale (FRM) to S Maouche, and founding from the French Ministry of Research.  ... 
doi:10.1186/1471-2164-9-302 pmid:18578872 pmcid:PMC2464609 fatcat:mlxfkp3einagfkjt5ug675gjru

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

Fu-Yuan Zhu, Mo-Xian Chen, Neng-Hui Ye, Wang-Min Qiao, Bei Gao, Wai-Ki Law, Yuan Tian, Dong Zhang, Di Zhang, Tie-Yuan Liu, Qi-Juan Hu, Yun-Ying Cao (+3 others)
2018 Plant Methods  
Results: The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter-(correlation, 0.88-0.93) and intra-platform (correlation, 0.95-0.98) comparison for gene  ...  The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated.  ...  Summary of gene and transcript identification. Acknowledgements We thank Ms. HHKAchala in providing language editing on this manuscript.  ... 
doi:10.1186/s13007-018-0337-0 pmid:30123314 pmcid:PMC6088413 fatcat:pcjbnovt4ndiripw6evk3nigke

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples

Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Maximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
2017 BMC Genomics  
We concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost.  ...  Conclusions: Despite the fact that the results of gene expression analysis were highly consistent between Human Transcriptome Arrays and RNA-seq platforms, the analysis of alternative splicing produced  ...  Availability of data and materials Tables with differentially expressed mRNAs and lncRNAs, enriched GO terms and common splicing events are available in Additional files 2, 3 and 4.  ... 
doi:10.1186/s12864-017-3819-y pmid:28587590 pmcid:PMC5461714 fatcat:ylnud2ijxzhzji6r3nyhjdv4om

The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome

Eric R Londin, Eleftheria Hatzimichael, Phillipe Loher, Leonard Edelstein, Chad Shaw, Kathleen Delgrosso, Paolo Fortina, Paul F Bray, Steven E McKenzie, Isidore Rigoutsos
2014 Biology Direct  
We profiled the platelet transcriptome of 10 healthy young males (5 white and 5 black) with no notable clinical history using RNA sequencing and by Affymetrix microarray.  ...  For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes' relationship is  ...  The work was supported in part by a William M. Keck Foundation grant (IR) and HL102482 from the National Heart, Lung and Blood Institute of the National Institutes of Health (PB).  ... 
doi:10.1186/1745-6150-9-3 pmid:24524654 pmcid:PMC3937023 fatcat:26lcwpj3bzcttkppbhul7fv5hu

Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease

Francisco Azuaje, Huiru Zheng, Anyela Camargo, Haiying Wang
2011 Journal of Biomedical Informatics  
However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis.  ...  We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain.  ...  Inter-dataset, process-oriented concordance of putative biomarker discovery methods After investigating the intra-dataset agreement between methods, we characterized each dataset according to the GO Biological  ... 
doi:10.1016/j.jbi.2011.02.003 pmid:21315182 fatcat:2rd2d6yiinhg5cadfkzobd3tyi

Variability of DNA microarray gene expression profiles in cultured rat primary hepatocytes

Jun Xu, Xutao Deng, Victor Chan, Nancy Kelley-Loughnane, Brent W Harker, Leming Shi, Saber M Hussain, John M Frazier, Charles Wang
2007 Gene Regulation and Systems Biology  
In addition, the impact of sample size on the variability of differentially expressed gene lists and the consistency of biological responses were also investigated.  ...  The reproducibility of gene lists and their functional classification was declined considerably when the sample size was decreased.  ...  Hong Fang of the National Center for Toxicological Research, Jefferson, AR for conducting a 3-way ANOVA analysis using the Partek software for us. We are grateful to Dr. Jaroslav P.  ... 
pmid:19936092 pmcid:PMC2759134 fatcat:gkfttwl7bnclvglc2qctrar5fq

Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits

Anna J. Jasinska, Susan Service, Oi-wa Choi, Joseph DeYoung, Olivera Grujic, Sit-yee Kong, Matthew J. Jorgensen, Julia Bailey, Sherry Breidenthal, Lynn A. Fairbanks, Roger P. Woods, J. David Jentsch (+1 others)
2009 Human Molecular Genetics  
The high heritability of levels of these transcripts in a large vervet pedigree validated our approach of focusing on transcripts that showed higher inter-individual compared with intra-individual variation  ...  Given the high degree of conservation of tissue expression profiles between vervets and humans, our findings may facilitate the understanding of regional and individual transcriptional variation and its  ...  Briefly, this tool maps the gene list of interest to the Panther ontology and compares to the selected reference gene list to identify over-and under-represented terms.  ... 
doi:10.1093/hmg/ddp397 pmid:19692348 pmcid:PMC2766297 fatcat:3wiwlehznzd4vjpoenkodnmrkm

Common DNA methylation alterations of Alzheimer's disease and aging in peripheral whole blood

Hongdong Li, Zheng Guo, You Guo, Mengyao Li, Haidan Yan, Jun Cheng, Chenguang Wang, Guini Hong
2016 OncoTarget  
The PWB Age-CpGs and AD-CpGs significantly overlapped 107 sites (P-value = 2.61×10 -12 ) and 97 had significantly concordant methylation alterations in AD and aging (P-value < 2.2×10 -16 ), which were  ...  However, the origin of PWB biomarkers is still controversial.  ...  CoNFlICTS oF INTEREST The authors declare there are no potential conflicts of interest.  ... 
doi:10.18632/oncotarget.7862 pmid:26943045 pmcid:PMC4991367 fatcat:tcfwq5tbejbwlkioxa5bxz46pa

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

Morten Rye, Geir Sandve, Carsten O Daub, Hideya Kawaji, Piero Carninci, Alistair RR Forrest, Finn Drabløs
2014 BMC Genomics  
In particular we find a substantial number of repressed inter-and intra-genic transcription start sites enriched for active chromatin marks and Pol II, and these sites are strongly associated with immediate-early  ...  Results: Transcription start sites can be distinguished by chromatin states defined by specific combinations of both chromatin mark enrichment and the profile shapes of these chromatin marks.  ...  We would like to thank all members of the FANTOM5 consortium for contributing to generation of samples and analysis of the data-set and thank GeNAS for data production.  ... 
doi:10.1186/1471-2164-15-120 pmid:24669905 pmcid:PMC3986914 fatcat:tfwnyhfy2bafjic2btyka3jtyu

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

Fang Liu, Tor-Kristian Jenssen, Jeff Trimarchi, Claudio Punzo, Connie L Cepko, Lucila Ohno-Machado, Eivind Hovig, Winston Patrick Kuo
2007 BMC Genomics  
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 8: 153.  ...  As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel  ...  WPK was supported by the National Institutes of Health (NIH) EY014466 grant, the Bioinformatics Division of the Harvard Center for Neurodegeneration and Repair and Harvard School of Dental Medicine Dean  ... 
doi:10.1186/1471-2164-8-153 pmid:17555589 pmcid:PMC1899500 fatcat:a2ckgkv7fzgk5hmea7t2mzabqa

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis

Caralina Marín de Evsikova, Isaac D. Raplee, John Lockhart, Gilberto Jaimes, Alexei V. Evsikov
2019 Journal of Personalized Medicine  
The cost and time required for transcriptome analysis has been greatly reduced by the development of next generation sequencing.  ...  The goal of this resource article is to provide background and a guide to appropriate technologies and downstream analyses in transcriptomics experiments generating ever-increasing amounts of gene expression  ...  (C) Number of genes annotated with at least one GO term in the species. Figure 7 . 7 Examples of ontology structure and the power of ontological analysis.  ... 
doi:10.3390/jpm9020021 pmid:31032818 pmcid:PMC6617151 fatcat:zdwuzaf2ynevpldukzwdnvnbhu

Novel Insights into DNA Methylation Features in Spermatozoa: Stability and Peculiarities

Csilla Krausz, Juan Sandoval, Sergi Sayols, Chiara Chianese, Claudia Giachini, Holger Heyn, Manel Esteller, Joel R. Drevet
2012 PLoS ONE  
The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same  ...  Our description about a highly polarized sperm DNA methylation profile, the clearly distinct genomic and functional organization of hypo- versus hypermethylated loci as well as the association of histone-enriched  ...  We thank Sue Hammoud and Doug Carrell (University of Utah, Salt lake City, USA) for providing us with their data regarding the histone-enriched loci.  ... 
doi:10.1371/journal.pone.0044479 pmid:23071498 pmcid:PMC3467000 fatcat:gjlkrdww3zfwxhry2gtkqk72zu

Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer

Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y. Seiwert, Ezra E. W. Cohen, H. Rosie Xing, Yves A. Lussier, Roland L. Dunbrack
2012 PLoS Computational Biology  
FAIME, the Functional Analysis of Individual Microarray Expression, computes mechanism scores using rank-weighted gene expression of an individual sample.  ...  To increase the utility of multi-gene signatures in survival studies, we developed a novel approach to generate "personal mechanism signatures" of molecular pathways and functions from gene expression  ...  the intra-subcategory relationships of the KEGG and GO terms inherited from the genes.  ... 
doi:10.1371/journal.pcbi.1002350 pmid:22291585 pmcid:PMC3266878 fatcat:arokoinhbvd6jpk5xxv73eosjm

iPhemap: an atlas of phenotype to genotype relationships of human iPSC models of neurological diseases

Ethan W Hollingsworth, Jacob E Vaughn, Josh C Orack, Chelsea Skinner, Jamil Khouri, Sofia B Lizarraga, Mark E Hester, Fumihiro Watanabe, Kenneth S Kosik, Jaime Imitola
2017 EMBO Molecular Medicine  
Overall, our findings offer new insights into the phenogenetics of iPSC-derived models while our web tool provides a platform for researchers to query and deposit phenotypic information of neurological  ...  Here, we report a systematic analysis of research practices and reporting bias in neurological disease models from 93 published articles.  ...  Acknowledgements The authors thank Drs. Christopher A. Walsh  ... 
doi:10.15252/emmm.201708191 pmid:29051230 pmcid:PMC5731211 fatcat:4ne2ly6rzfccdjbcuu36ahld74
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