Gene ontology analysis for RNA-seq: accounting for selection bias

Keywords

Biology, RNA-Seq, Gene ontology, Human genetics, Computational biology

References

• BIASED SAMPLING; THE NONCENTRAL HYPERGEOMETRIC PROBABILITY DISTRIBUTIONKenneth T. Wallenius — 1963
• Bioinformatics and Computational Biology Solutions Using R and BioconductorRobert Gentleman, Irizarry, Rafael A, Huber, Wolfgang — 2006
• Transcriptional programs activated by exposure of human prostate cancer cells to androgenSamuel E. DePrimo, Maximilian Diehn, Joel B. Nelson — 2002
• Weighted random sampling with a reservoirPavlos S. Efraimidis, Paul G. Spirakis — 2006
• The development of androgen-independent prostate cancerBrian J. Feldman, David Feldman — 2001
• Large-scale mRNA sequencing determines global regulation of RNA editing during brain development.Helene Wahlstedt, Chammiran Daniel, Mats Ensterö — 2009
• EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical speciesXin Zhou, Zhen Su — 2007
• Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer modelHairi Li, Michael Lovci, Young‐Soo Kwon — 2008
• GOstat: find statistically overrepresented Gene Ontologies within a group of genes.Tim Beißbarth, Terence P. Speed — 2004
• Gene Ontology: tool for the unification of biologyMichael Ashburner, Catherine A. Ball, Judith A. Blake — 2000
• A scaling normalization method for differential expression analysis of RNA-seq dataMark D. Robinson, Alicia Oshlack — 2010
• Controlling the false discovery rate: a practical and powerful approach to multiple testingYoav Benjamini, Yosef Hochberg — 1995
• Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse BrainXu Wang, Qi Sun, Sean McGrath — 2008
• edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataMark D. Robinson, Davis J. McCarthy, Gordon K. Smyth — 2009
• Transcript length bias in RNA-seq data confounds systems biologyAlicia Oshlack, Matthew J. Wakefield — 2009
• Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platformsPeter A.C. ’t Hoen, Yavuz Ariyürek, Helene Thygesen — 2008
• RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.John C. Marioni, Christopher E. Mason, Shrikant Mane — 2008
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeBen Langmead, Cole Trapnell, Mihai Pop — 2009
• From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesAravind Subramanian, Pablo Tamayo, Vamsi K. Mootha — 2005
• GOToolBox: functional analysis of gene datasets based on Gene OntologyDavid Martin, Christine Brun, Élisabeth Rémy — 2004

Cited by

• The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in ChlamydomonasChia‐Hong Tsai, Jaruswan Warakanont, Tomomi Takeuchi — 2014
• Seed genome hypomethylated regions are enriched in transcription factor genesMin Chen, Jer-Young Lin, Jungim Hur — 2018
• Heterologous Expression of a Novel Zoysia japonica C2H2 Zinc Finger Gene, ZjZFN1, Improved Salt Tolerance in ArabidopsisKe Teng, Penghui Tan, Weier Guo — 2018
• An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen AvailabilityXin Wei, Lina Zhang, Wenzhong Zhang — 2019
• Why is the world not a much better place now that so much more information is available?Norman Sartorius — 2007
• Single-base resolution methylomes of cotton CMS system reveal epigenomic changes in response to high-temperature stress during anther development.Meng Zhang, Xuexian Zhang, Liping Guo — 2019
• Management of sterile necrosis in instances of severe acute pancreatitis.Beate Rau, U. Pralle, Waldemar Uhl — 1995
• Socialinės atsakomybės įtvirtinimo potencialo verslo organizacijose vertinimasJovita Seiliūtė, Danuta Diskienė, Albinas Marčinskas — 2013
• [Laparoscopic mini gastric bypass for the treatment of morbid obesity. Initial experience].Cătălin Copăescu, R Munteanu, N Prala — 2004
• Investigation of vectorized Monte Carlo AlgorithmsF.B. Brown, D. A. Calahan, William R. Martin — 1981
• El 15M como insurrección del cuerpo-máquinaRaúl Sánchez Cedillo — 2012
• The evolution of stress response and complex life history traits in natural populations of garter snakesTonia S. Schwartz — 2012
• Examination of the expression of genes and proteins controlling M. longissimus thoracis et lumborum growth in steersS.M. Keady — 2011
• Roots Facing Water Deficit: Abscisic Acid Plays a Key Role in Mediating Stress Avoidance in PoplarGiovanni Zaccaria — 2014
• Bioinformatics Software and Methods for Genome-wide Association and ChIP-Seq Studies.Ryan Welch — 2013
• MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysisKoki Tsuyuzaki, Gota Morota, Manabu Ishii — 2015
• Histone Demethylation Maintains Prdm14 and Tsix Expression and Represses Xist in Embryonic Stem CellsYasunao Kamikawa, Mary E. Donohoe — 2015
• Creatine Deficiency Syndromes: A Clinical, Molecular and Functional ApproachJoseph Ndika — 2014
• Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses with RNA sequencingThanh Hoang, Praveen Kumar, Sutharzan Sreeskandarajan — 2014
• A Human-Specific α7-Nicotinic Acetylcholine Receptor Gene in Human Leukocytes: Identification, Regulation and the Consequences of CHRFAM7A ExpressionTodd W. Costantini, Xitong Dang, Maryana V Yurchyshyna — 2015

Related papers

• FOXM1 binds directly to non-consensus sequences in the human genomeDeborah A. Sanders, Michael V. Gormally, Giovanni Marsico — 2015
• The many uses of a genome sequenceAnna Sharman — 2001
• Comparative genomics of Drosophila and human core promotersPeter Fitzgerald, David Sturgill, Andrey Shyakhtenko — 2006
• Q & A: the SnyderomeM Snyder — 2012
• When (distant) relatives stay too long: implications for cancer medicineDiego Chowell, Amy M. Boddy, Diego Mallo — 2016
• Out of AfricaGregory A. Petsko — 2012
• Single Cell Genomics meeting in Stockholm: from single cells to cell typesAntonio Scialdone, Kaia Achim, John C. Marioni — 2014
• Next-generation human geneticsJay Shendure — 2011