Spectrum structures and biological functions of 8-mers in the human genome.
Identifieur interne : 000377 ( Main/Exploration ); précédent : 000376; suivant : 000378Spectrum structures and biological functions of 8-mers in the human genome.
Auteurs : Yun Jia [République populaire de Chine] ; Hong Li [République populaire de Chine] ; Jingfeng Wang [République populaire de Chine] ; Hu Meng [République populaire de Chine] ; Zhenhua Yang [République populaire de Chine]Source :
- Genomics [ 1089-8646 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : Nucléosomes.
- Analyse de séquence d'ADN, Biologie informatique, Génome humain, Humains, Ilots CpG, Motifs nucléotidiques.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Nucleosomes.
- Computational Biology, CpG Islands, Genome, Human, Humans, Nucleotide Motifs, Sequence Analysis, DNA.
Abstract
The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.
DOI: 10.1016/j.ygeno.2018.03.006
PubMed: 29522801
Affiliations:
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We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Jia, Yun" sort="Jia, Yun" uniqKey="Jia Y" first="Yun" last="Jia">Yun Jia</name></noRegion><name sortKey="Li, Hong" sort="Li, Hong" uniqKey="Li H" first="Hong" last="Li">Hong Li</name><name sortKey="Meng, Hu" sort="Meng, Hu" uniqKey="Meng H" first="Hu" last="Meng">Hu Meng</name><name sortKey="Wang, Jingfeng" sort="Wang, Jingfeng" uniqKey="Wang J" first="Jingfeng" last="Wang">Jingfeng Wang</name><name sortKey="Yang, Zhenhua" sort="Yang, Zhenhua" uniqKey="Yang Z" first="Zhenhua" last="Yang">Zhenhua Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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