PFGD: A systematic functional genomics resource for Poplar

Jingna Si, Jin Cheng, Rongling Wu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

As the model species for woody plants, the poplar has excellent experimental properties. The studies of functional genes make up the foundation of improving genetic traits and cultivating elite lines at the molecular level. Although studies of functional genes have been carried out for many years, plenty of experimental data are still scattered across documents and are not unified by a comprehensive statistical analysis, Consequentially, the disjoint in information severely hinders systematic utilization of the accumulated data. This problem can be solved through the use of bioinformatic methodology and technology to gather and organize data to construct this Poplar Functional Gene Database (PFGD). By complining information from an array of studies, this study collected 207 poplar functional genes. 164 of the collected genes, selected for their detailed annotations, were input into Populus Database (http://ccb.bjfu.edu.cn/app/pfgd/). Many important stress genes were located in the database. As an example, we investigate the target genes function of Populus euphratica in response to salt stress. Two small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in the root. Using high-throughput sequencing to identify miRNAs, we found 179 conserved miRNAs and 62 novel miRNAs which have differential expression. After the detailed analysis of these miRNAs, 1254 target genes from conserved miRNAs and 479 target genes from novel miRNAs were predicted, and functional information was annotated using the Gene Ontology databases. These information provides a primary visual field for understanding the gene regulatory network in response to salt stress in Populus.

Original languageEnglish (US)
Title of host publicationProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
EditorsHuiru Zheng, Xiaohua Tony Hu, Yadong Wang, Jin-Kao Hao, David Gilbert, Daniel Berrar, Kwang-Hyun Cho, Werner Dubitzky
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages18-22
Number of pages5
ISBN (Electronic)9781479956692
DOIs
StatePublished - Dec 29 2014
Event2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom
Duration: Nov 2 2014Nov 5 2014

Publication series

NameProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Other

Other2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
CountryUnited Kingdom
CityBelfast
Period11/2/1411/5/14

Fingerprint

Genomics
Genes
Databases
MicroRNAs
Populus
Salts
Gene Ontology
Gene Regulatory Networks
Computational Biology
Visual Fields
Gene Library
Bioinformatics
Application programs
Ontology
Statistical methods
Technology
Throughput

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics

Cite this

Si, J., Cheng, J., & Wu, R. (2014). PFGD: A systematic functional genomics resource for Poplar. In H. Zheng, X. T. Hu, Y. Wang, J-K. Hao, D. Gilbert, D. Berrar, K-H. Cho, ... W. Dubitzky (Eds.), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 (pp. 18-22). [6999298] (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2014.6999298
Si, Jingna ; Cheng, Jin ; Wu, Rongling. / PFGD : A systematic functional genomics resource for Poplar. Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. editor / Huiru Zheng ; Xiaohua Tony Hu ; Yadong Wang ; Jin-Kao Hao ; David Gilbert ; Daniel Berrar ; Kwang-Hyun Cho ; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 18-22 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).
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Si, J, Cheng, J & Wu, R 2014, PFGD: A systematic functional genomics resource for Poplar. in H Zheng, XT Hu, Y Wang, J-K Hao, D Gilbert, D Berrar, K-H Cho & W Dubitzky (eds), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014., 6999298, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Institute of Electrical and Electronics Engineers Inc., pp. 18-22, 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Belfast, United Kingdom, 11/2/14. https://doi.org/10.1109/BIBM.2014.6999298

PFGD : A systematic functional genomics resource for Poplar. / Si, Jingna; Cheng, Jin; Wu, Rongling.

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. ed. / Huiru Zheng; Xiaohua Tony Hu; Yadong Wang; Jin-Kao Hao; David Gilbert; Daniel Berrar; Kwang-Hyun Cho; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. p. 18-22 6999298 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Si J, Cheng J, Wu R. PFGD: A systematic functional genomics resource for Poplar. In Zheng H, Hu XT, Wang Y, Hao J-K, Gilbert D, Berrar D, Cho K-H, Dubitzky W, editors, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. Institute of Electrical and Electronics Engineers Inc. 2014. p. 18-22. 6999298. (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). https://doi.org/10.1109/BIBM.2014.6999298