Mining Regulatory Elements in Non-coding Regions of Arabidopsis thaliana

被引:2
|
作者
Li, Xi [1 ]
Wang, Dianhui [1 ]
机构
[1] La Trobe Univ, Dept Comp Sci & Comp Engn, Melbourne, Vic 3086, Australia
来源
COMPUTATIONAL SYSTEMS-BIOLOGY AND BIOINFORMATICS | 2010年 / 115卷
关键词
Evolutionary computation; regulatory element; Arabidopsis thaliana; GENETIC ALGORITHM; DISCOVERY; SITES;
D O I
10.1007/978-3-642-16750-8_9
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Analysis of regulatory elements (DNA motifs) in non-coding regions is considered as one crucial step to understand the regulation mechanisms of genes with similar expression patterns. With the help of accumulated gene expression data and complete genome sequences, computational approaches have been developed in the past decade to accelerate the mining task. In previous studies, we proposed a DNA motif discovery framework, named as MODEC, which incorporated the evolutionary computation (EC) searching algorithm with data filtering techniques to favor the algorithm performance. With the attempt on exploring real-world motif mining problems, we apply both MODEC and a famous discovery algorithm MEME to predict regulatory elements in different non-coding regions of co-expressed genes from the model plant Arabidopsis thaliana. Results from both MODEC and MEME show that the targeted motif patterns can be found in the expected non-coding regions of the co-expressed gene groups. As the preliminary step of this work, we investigate whether different motif patterns can be detected in the specified non-coding regions of co-expressed genes with different functional categories. The similar prediction results from MODEC and MEME demonstrate the potential of MODEC in the field of practical motif discovery.
引用
收藏
页码:94 / 105
页数:12
相关论文
共 50 条
  • [21] Targeted resequencing of coding and cardiac non-coding regulatory regions related to genes implicated in cardiomyopathy
    Nagyova, E.
    Harakalova, M.
    Tragante, V.
    Kummeling, G.
    Sammani, A.
    Verdonschot, J. A. J.
    Baas, A.
    Van den Velden, J.
    Mokry, M.
    Asselbergs, F. W.
    CARDIOVASCULAR RESEARCH, 2018, 114 : S19 - S19
  • [22] Discriminating coding, non-coding and regulatory regions using rescaled range and detrended fluctuation analysis
    te Boekhorst, Rene
    Abnizova, Irina
    Nehaniv, Chrystopher
    BIOSYSTEMS, 2008, 91 (01) : 183 - 194
  • [23] Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana
    Antonio Corona-Gomez, Jose
    Lorena Coss-Navarrete, Evelia
    Jair Garcia-Lopez, Irving
    Klapproth, Christopher
    Alejandro Perez-Patino, Jaime
    Fernandez-Valverde, Selene L.
    SCIENTIFIC REPORTS, 2022, 12 (01)
  • [24] Integrative identification of non-coding regulatory regions driving metastatic prostate cancer
    Woo, Brian J.
    Moussavi-Baygi, Ruhollah
    Karner, Heather
    Karimzadeh, Mehran
    Yousefi, Hassan
    Lee, Sean
    Garcia, Kristle
    Joshi, Tanvi
    Yin, Keyi
    Navickas, Albertas
    Gilbert, Luke A.
    Wang, Bo
    Asgharian, Hosseinali
    Feng, Felix Y.
    Goodarzi, Hani
    CELL REPORTS, 2024, 43 (09):
  • [25] Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana
    Jose Antonio Corona-Gomez
    Evelia Lorena Coss-Navarrete
    Irving Jair Garcia-Lopez
    Christopher Klapproth
    Jaime Alejandro Pérez-Patiño
    Selene L. Fernandez-Valverde
    Scientific Reports, 12
  • [26] DNA methylation to identify non-coding gene regulatory regions in tumor samples
    Berman, Benjamin P.
    CANCER RESEARCH, 2015, 75
  • [27] Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis and phenotypes
    Stefanucci, Luca
    Frontini, Mattia
    JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 2022, 20 (08) : 1759 - 1765
  • [28] UCNEbase-a database of ultraconserved non-coding elements and genomic regulatory blocks
    Dimitrieva, Slavica
    Bucher, Philipp
    NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D101 - D109
  • [29] Non-coding transcription at cis-regulatory elements: Computational and experimental approaches
    Simonatto, Marta
    Barozzi, Iros
    Natoli, Gioacchino
    METHODS, 2013, 63 (01) : 66 - 75
  • [30] Role of Conserved Non-Coding Regulatory Elements in LMW Glutenin Gene Expression
    Juhasz, Angela
    Makai, Szabolcs
    Sebestyen, Endre
    Laszlo Tamas
    Balazs, Ervin
    PLOS ONE, 2011, 6 (12):