References
- Jung BC, Kang S. Epigenetic regulation of inflammatory factors in adipose tissue. Biochim Biophys Acta Mol Cell Biol Lipids. 2021;1866:159019. https://doi.org/10.1016/j.bbalip.2021.159019
- Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545-15550. https://doi.org/10.1073/pnas.0506580102
- Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467-470. https://doi.org/10.1126/science.270.5235.467
- Mutz KO, Heilkenbrinker A, Lonne M, Walter JG, Stahl F. Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol. 2013;24:22-30. https://doi.org/10.1016/j.copbio.2012.09.004
- Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One. 2014;9:e78644. https://doi.org/10.1371/journal.pone.0078644
- Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet. 2019;20:631-656. https://doi.org/10.1038/s41576-019-0150-2
- Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63. https://doi.org/10.1038/nrg2484
- Sigurgeirsson B, Emanuelsson O, Lundeberg J. Sequencing degraded RNA addressed by 3' tag counting. PLoS One. 2014;9:e91851. https://doi.org/10.1371/journal.pone.0091851
- Jung BC, You D, Lee I, Li D, Schill RL, Ma K, et al. TET3 plays a critical role in white adipose development and diet-induced remodeling. Cell Rep. 2023;42:113196. https://doi.org/10.1016/j.celrep.2023.113196
- Weng X, Juenger TE. A high-throughput 3'-Tag RNA sequencing for large-scale time-series transcriptome studies. Methods Mol Biol. 2022;2398:151-172. https://doi.org/10.1007/978-1-0716-1912-4_13
- Wu X, Bartel DP. Widespread influence of 3'-end structures on mammalian mRNA processing and stability. Cell. 2017;169:905-917.e11. https://doi.org/10.1016/j.cell.2017.04.036
- Raghavan V, Kraft L, Mesny F, Rigerte L. A simple guide to de novo transcriptome assembly and annotation. Brief Bioinform. 2022;23:bbab563. https://doi.org/10.1093/bib/bbab563
- Liao X, Li M, Zou Y, Wu FX, Yi P, Wang J. Current challenges and solutions of de novo assembly. Quant Biol. 2019;7:90-109. https://doi.org/10.1007/s40484-019-0166-9
- Teo YY. Exploratory data analysis in large-scale genetic studies. Biostatistics. 2010;11:70-81. https://doi.org/10.1093/biostatistics/kxp038
- Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, et al. A beginner's guide to analysis of RNA sequencing data. Am J Respir Cell Mol Biol. 2018;59:145-157. https://doi.org/10.1165/rcmb.2017-0430tr
- Chen X, Zhang B, Wang T, Bonni A, Zhao G. Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. BMC Bioinformatics. 2020;21:269. https://doi.org/10.1186/s12859-020-03608-0
- Ringner M. What is principal component analysis? Nat Biotechnol. 2008;26:303-304. https://doi.org/10.1038/nbt0308-303
- Jolliffe IT, Cadima J. Principal component analysis: a review and recent developments. Philos Trans A Math Phys Eng Sci. 2016;374:20150202. https://doi.org/10.1098/rsta.2015.0202
- Khomtchouk BB, Van Booven DJ, Wahlestedt C. HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. Source Code Biol Med. 2014;9:30. https://doi.org/10.1186/s13029-014-0030-2
- Engle S, Whalen S, Joshi A, Pollard KS. Unboxing cluster heatmaps. BMC Bioinformatics. 2017;18(Suppl 2):63. https://doi.org/10.1186/s12859-016-1442-6
- Gu Z. Complex heatmap visualization. iMeta. 2022;1:e43. https://doi.org/10.1002/imt2.43
- El Bouchefry K, de Souza RS. Learning in big data: introduction to machine learning. In: Skoda P, Adam F, editors. Knowledge discovery in big data from astronomy and earth observation: AstroGeoInformatics. Elsevier: 2020. p. 225-249.
- Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847-2849. https://doi.org/10.1093/bioinformatics/btw313
- Li W. Volcano plots in analyzing differential expressions with mRNA microarrays. J Bioinform Comput Biol. 2012;10:1231003. https://doi.org/10.1142/s0219720012310038
- Ebrahimpoor M, Goeman JJ. Inflated false discovery rate due to volcano plots: problem and solutions. Brief Bioinform. 2021;22:bbab053. https://doi.org/10.1093/bib/bbab053
- Bedre R. reneshbedre/bioinfokit: bioinformatics data analysis and visualization toolkit [Internet]. Zenodo [cited 2022 Sep 4]. Available from: https://doi.org/10.5281/zenodo.3698145
- Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010;11:733-739. https://doi.org/10.1038/nrg2825
- Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, et al. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nat Protoc. 2019;14:482-517. https://doi.org/10.1038/s41596-018-0103-9
- Garcia-Campos MA, Espinal-Enriquez J, Hernandez-Lemus E. Pathway analysis: state of the art. Front Physiol. 2015;6:383. https://doi.org/10.3389/fphys.2015.00383
- Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012;8:e1002375. https://doi.org/10.1371/journal.pcbi.1002375
- Jung SH. Stratified Fisher's exact test and its sample size calculation. Biom J. 2014;56:129-140. https://doi.org/10.1002/bimj.201300048
- Dudoit S, Shaffer JP, Boldrick JC. Multiple hypothesis testing in microarray experiments. Stat Sci. 2003;18:71-103. https://doi.org/10.1214/ss/1056397487
- Camargo A, Azuaje F, Wang H, Zheng H. Permutation - based statistical tests for multiple hypotheses. Source Code Biol Med. 2008;3:15. https://doi.org/10.1186/1751-0473-3-15
- Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med. 1990;9:811-818. https://doi.org/10.1002/sim.4780090710
- Xie C, Jauhari S, Mora A. Popularity and performance of bioinformatics software: the case of gene set analysis. BMC Bioinformatics. 2021;22:191. https://doi.org/10.1186/s12859-021-04124-5
- Fang Z, Liu X, Peltz G. GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. Bioinformatics. 2023;39:btac757. https://doi.org/10.1093/bioinformatics/btac757
- Tamayo P, Steinhardt G, Liberzon A, Mesirov JP. The limitations of simple gene set enrichment analysis assuming gene independence. Stat Methods Med Res. 2016;25:472-487. https://doi.org/10.1177/0962280212460441
- Wang Y, Li J, Huang D, Hao Y, Li B, Wang K, et al. Comparing Bayesian-based reconstruction strategies in topology-based pathway enrichment analysis. Biomolecules. 2022;12:906. https://doi.org/10.3390/biom12070906
- Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, et al. A novel signaling pathway impact analysis. Bioinformatics. 2009;25:75-82. https://doi.org/10.1093/bioinformatics/btn577
- Grassi M, Tarantino B. SEMgsa: topology-based pathway enrichment analysis with structural equation models. BMC Bioinformatics. 2022;23:344. https://doi.org/10.1186/s12859-022-04884-8
- Ma J, Shojaie A, Michailidis G. A comparative study of topology-based pathway enrichment analysis methods. BMC Bioinformatics. 2019;20:546. https://doi.org/10.1186/s12859-019-3146-1
- Ibrahim MA, Jassim S, Cawthorne MA, Langlands K. A topology-based score for pathway enrichment. J Comput Biol. 2012;19:563-573. https://doi.org/10.1089/cmb.2011.0182
- Zhao K, Rhee SY. Interpreting omics data with pathway enrichment analysis. Trends Genet. 2023;39:308-319. https://doi.org/10.1016/j.tig.2023.01.003
- Nguyen TM, Shafi A, Nguyen T, Draghici S. Identifying significantly impacted pathways: a comprehensive review and assessment. Genome Biol. 2019;20:203. https://doi.org/10.1186/s13059-019-1790-4