Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example

作者: Najla Ksouri , Jaime A Castro-Mondragón , Francesc Montardit-Tardà , Jacques van Helden , Bruno Contreras-Moreira

DOI: 10.1093/PLPHYS/KIAA091

关键词:

摘要: … The name of the best match among plant motifs in footprintDB is labeled in red, next to its Ncor value labeled in blue. The x-axis corresponds to the module of interest (M41) and random …

参考文章(71)
Xiong-wei Li, Jun Jiang, Li-ping Zhang, Yi Yu, Zheng-wen Ye, Xiu-min Wang, Jing-yi Zhou, Ming-liang Chai, Hui-qin Zhang, Pere Arús, Hui-juan Jia, Zhong-shan Gao, Identification of volatile and softening-related genes using digital gene expression profiles in melting peach Tree Genetics & Genomes. ,vol. 11, pp. 71- ,(2015) , 10.1007/S11295-015-0891-9
Valmor J. Bianchi, Manuel Rubio, Livio Trainotti, Ignazio Verde, Claudio Bonghi, Pedro Martínez-Gómez, Prunus transcription factors: breeding perspectives. Frontiers in Plant Science. ,vol. 6, pp. 443- 443 ,(2015) , 10.3389/FPLS.2015.00443
Peter Langfelder, Steve Horvath, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. ,vol. 9, pp. 559- 559 ,(2008) , 10.1186/1471-2105-9-559
Shisong Ma, Smit Shah, Hans J. Bohnert, Michael Snyder, Savithramma P. Dinesh-Kumar, Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways PLoS Genetics. ,vol. 9, pp. e1003840- ,(2013) , 10.1371/JOURNAL.PGEN.1003840
Wen-Chi Chang, Tzong-Yi Lee, Hsien-Da Huang, His-Yuan Huang, Rong-Long Pan, PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups BMC Genomics. ,vol. 9, pp. 561- 561 ,(2008) , 10.1186/1471-2164-9-561
Matthew Slattery, Roumen Voutev, Lijia Ma, Nicolas Nègre, Kevin P. White, Richard S. Mann, Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning PLoS Genetics. ,vol. 9, pp. e1003753- 17 ,(2013) , 10.1371/JOURNAL.PGEN.1003753
Christophe Liseron-Monfils, Tim Lewis, Daniel Ashlock, Paul D McNicholas, François Fauteux, Martina Strömvik, Manish N Raizada, Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas BMC Plant Biology. ,vol. 13, pp. 42- 42 ,(2013) , 10.1186/1471-2229-13-42
José M. Franco-Zorrilla, Irene López-Vidriero, José L. Carrasco, Marta Godoy, Pablo Vera, Roberto Solano, DNA-binding specificities of plant transcription factors and their potential to define target genes Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 2367- 2372 ,(2014) , 10.1073/PNAS.1316278111
J. van Helden, B. André, J. Collado-Vides, Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies Journal of Molecular Biology. ,vol. 281, pp. 827- 842 ,(1998) , 10.1006/JMBI.1998.1947