TY - JOUR
T1 - PlaMoM
T2 - A comprehensive database compiles plant mobile macromolecules
AU - Guan, Daogang
AU - Yan, Bin
AU - Thieme, Christoph
AU - Hua, Jingmin
AU - Zhu, Hailong
AU - Boheler, Kenneth R.
AU - Zhao, Zhongying
AU - Kragler, Friedrich
AU - Xia, Yiji
AU - Zhang, Shoudong
N1 - Funding information:
Hong Kong Baptist University start-up fund [38-40-160 to S.Z., 38-40-159 to D.G.]; HKBU FRG grants [FRG1/14-15/055, FRG2/15-16/006 to S.Z., FRG1/14-15/070 to D.G.]; National Nature Science Foundation of China [31501080 to D.G.]; HKBU Strategic Development Fund [SDF 15-1012-P04 to Y.X.]. Funding for open access charge: Hong Kong Baptist University start-up fund [38-40-160].
Publisher copyright:
© The Author(s) 2016.
PY - 2017/1
Y1 - 2017/1
N2 - In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein-protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/.
AB - In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein-protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/.
UR - https://doi.org/10.1093/nar/gkaa538
UR - http://www.scopus.com/inward/record.url?scp=85016096251&partnerID=8YFLogxK
U2 - 10.1093/nar/gkw988
DO - 10.1093/nar/gkw988
M3 - Article
C2 - 27924044
AN - SCOPUS:85016096251
SN - 0305-1048
VL - 45
SP - D1021-D1028
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -