POPE: pipeline of parentally-biased expression
作者： Victor Missirian , Isabelle Henry , Luca Comai , Vladimir Filkov
DOI: 10.1007/978-3-642-30191-9_17
关键词:
摘要: While one might expect the phenotypes of progeny to be an additive combination parents, Mendelian analysis reveals that this is not always case. Deviations from expectation are observable even at level gene expression, and identifying such instances a prerequisite understanding regulation networks. Many biological studies employ mRNA-seq identify where overall allelic expression in hybrids deviates expectation. We describe pipeline, POPE (Pipeline Parentally-biased Expression), capable detecting these instances, building off linear model terms regulatory sequence strength concentration synergistic transcriptional regulators. illustrate performance on existing data set. implemented entirely shell, python, R, it designed for unix-based platforms. The code can found http://www.cs.ucdavis. edu/~filkov/POPE/ .
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sci-hub.st 参考文章(27)
I. Tirosh, S. Reikhav, A. A. Levy, N. Barkai, A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation Science. ,vol. 324, pp. 659- 662 ,(2009) , 10.1126/SCIENCE.1169766
Thomas J Hardcastle, Krystyna A Kelly, baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data BMC Bioinformatics. ,vol. 11, pp. 422- 422 ,(2010) , 10.1186/1471-2105-11-422
Sergei A. Filichkin, Ghislain Breton, Henry D. Priest, Palitha Dharmawardhana, Pankaj Jaiswal, Samuel E. Fox, Todd P. Michael, Joanne Chory, Steve A. Kay, Todd C. Mockler, Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules PLoS ONE. ,vol. 6, pp. e16907- ,(2011) , 10.1371/JOURNAL.PONE.0016907
Ben Langmead, Kasper D Hansen, Jeffrey T Leek, None, Cloud-scale RNA-sequencing differential expression analysis with Myrna Genome Biology. ,vol. 11, pp. 1- 11 ,(2010) , 10.1186/GB-2010-11-8-R83
Alan F Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J Johnston, Jeffrey J Swensen, W Johnson, Barry Moore, Chad D Huff, Lynne M Bird, John C Carey, John M Opitz, Cathy A Stevens, Christa Schank, Heidi Fain, Reid Robison, Brian Dalley, Steven Chin, Sarah T South, Theodore J Pysher, Lynn B Jorde, Hakon Hakonarson, Johan R Lillehaug, Leslie G Biesecker, Mark Yandell, Thomas Arnesen, Gholson J Lyon, Massively parallel sequencing identifies a previously unrecognized X-linked disorder resulting in lethality in male infants owing to amino-terminal acetyltransferase deficiency Genome Biology. ,vol. 12, pp. 13- ,(2011) , 10.1186/GB-2011-12-S1-P13
Michael Carey, Young-Sun Lin, Michael R. Green, Mark Ptashne, A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature. ,vol. 345, pp. 361- 364 ,(1990) , 10.1038/345361A0
Zhongfu Ni, Eun-Deok Kim, Misook Ha, Erika Lackey, Jianxin Liu, Yirong Zhang, Qixin Sun, Z. Jeffrey Chen, Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids Nature. ,vol. 457, pp. 327- 331 ,(2009) , 10.1038/NATURE07523
Young-Sun Lin, Michael Carey, Mark Ptashne, Michael R. Green, How different eukaryotic transcriptional activators can cooperate promiscuously Nature. ,vol. 345, pp. 359- 361 ,(1990) , 10.1038/345359A0
Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher M. Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang, GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences PLoS ONE. ,vol. 6, pp. e25279- ,(2011) , 10.1371/JOURNAL.PONE.0025279
M. Groszmann, I. K. Greaves, Z. I. Albertyn, G. N. Scofield, W. J. Peacock, E. S. Dennis, Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor Proceedings of the National Academy of Sciences of the United States of America. ,vol. 108, pp. 2617- 2622 ,(2011) , 10.1073/PNAS.1019217108