Abstract：
KEY MESSAGE:We developed a machine learning-based model to identify the hidden labels of m6A candidates from noisy m6A-seq data. Peak-calling approaches, such as MeRIP-seq or m6A-seq, are commonly used to map m6A modifications. However, these technologies can only map m6A sites with 100-200 nt resolution and cannot reveal the precise location or the number of modified residues in a transcript. To address this challenge, we developed a novel machine learning-based approach, named HLMethy, to assign labels to m6A candidates from noisy m6A-seq data. The multiple instance learning framework was adopted and two different training strategies were used to generate the classification model. To test the performance of our model, the m6A sites with single-base resolution were used and our model achieved comparable performance against existing instance-level predictors, which suggest that our model has the potential to improve the data quality of m6A-seq at reduced costs. What's more, our generic framework can be extended to other newly found modifications that are found by peak-calling approaches. The source code of HLMethy is available at https://github.com/liuze-nwafu/HLMethy.
journal_name
Plant Mol Bioljournal_title
Plant molecular biologyauthors
Liu Z,Dong W,Luo W,Jiang W,Li Q,He Zdoi
10.1007/s11103-019-00930-xsubject
Has Abstractpub_date
2019-12-01 00:00:00pages
575-584issue
6eissn
0167-4412issn
1573-5028pii
10.1007/s11103-019-00930-xjournal_volume
101pub_type
杂志文章abstract：:Two wheat histone H2B genes (TH123 and TH153) were isolated. Nucleotide sequence analysis revealed that some characteristic sequence motifs were conserved in both the 5'- and 3'-flanking regions. A canonical TATA box and several CCAAT sequences were present in the presumed promoter regions. Motifs similar or identical...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00042047
更新日期：1995-04-01 00:00:00
abstract：:The synthesis of both strands of CaMV-DNA has been studied in vitro using viral replication complexes obtained by hypotonic extraction of infected plant organelles. Hybridization of the DNA synthesized in vitro to single stranded CaMV DNA probes cloned in bacteriophage M 13 confirmed that the 35 S RNA served as a temp...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00017779
更新日期：1984-09-01 00:00:00
abstract：:The microtubular element of the plant cytoskeleton undergoes dramatic architectural changes in the course of the cell cycle, specifically at the entry into and exit from mitosis. These changes underlie the acquisition of specialized properties and functions involved, for example, in the equal segregation of chromosome...
journal_title：Plant molecular biology
pub_type： 杂志文章,评审
doi：10.1023/a:1006346107807
更新日期：2000-08-01 00:00:00
abstract：:We identified a novel nucleoplasm localized protein in Arabidopsis called AT-hook motif nuclear localized protein 1 (AHL1), which was isolated by visual screening of transformants using random GFP::cDNA fusions. AHL1 contains an AT-hook motif and unknown conserved PPC (plants and prokaryotes conserved) domain that inc...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-004-3249-5
更新日期：2004-09-01 00:00:00
abstract：:The transcription factor ABA-Insensitive5 (ABI5) is a key regulator of ABA signaling and stress response in Arabidopsis seeds and seedlings. Potential ABI5-interacting proteins were identified by a yeast two-hybrid screen; the most prevalent interactors were a family of four highly conserved plant-specific proteins wi...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-008-9344-2
更新日期：2008-08-01 00:00:00
abstract：:Recent studies have revealed high sequence similarity between homospermidine synthase (HSS), the first pathway-specific enzyme in the biosynthesis of pyrrolizidine alkaloids, a class of sporadically occurring plant defence compounds, and deoxyhypusine synthase (DHS), a ubiquitous enzyme involved in the post-translatio...
journal_title：Plant molecular biology
pub_type： 杂志文章,评审
doi：10.1023/a:1026597621646
更新日期：2000-11-01 00:00:00
abstract：:A cDNA library from ethephon-treated cucumber cotyledons (Cucumis sativus L. cv. Poinsett 76) was constructed. Two cDNA clones encoding putative peroxidases were isolated by means of a synthetic probe based on a partial amino acid sequence of a 33 kDa cationic peroxidase that had been previously shown to be induced by...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00016504
更新日期：1990-05-01 00:00:00
abstract：:Plants count on a wide variety of metabolic, physiological, and developmental responses to adapt their growth to variations in mineral nutrient availability. To react to such variations plants have evolved complex sensing and signaling mechanisms that allow them to monitor the external and internal concentration of ea...
journal_title：Plant molecular biology
pub_type： 杂志文章,评审
doi：10.1007/s11103-008-9380-y
更新日期：2009-03-01 00:00:00
abstract：:The cytokinin gene, isopentenyl transferase (ipt), was placed under the control of a heat-inducible promoter from the Drosophila melanogaster hsp70 gene and introduced into Nicotiana plumbaginifolia by cocultivation with Agrobacterium tumefaciens. Transformants were analyzed for organ-specific expression, cytokinin le...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00017921
更新日期：1991-01-01 00:00:00
abstract：:Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture syst...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-006-9092-0
更新日期：2007-02-01 00:00:00
abstract：:Co-suppression of host genes and 35S transgenes encoding nitrate reductase was previously reported in transgenic tobacco plants (Nicotiana tabacum cv. Paraguay or Burley) using either a full-length cDNA or fragments devoid of the 3' and/or 5' UTR. Co-suppression was previously shown to affect a limited fraction of the...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00019126
更新日期：1995-10-01 00:00:00
abstract：:The nucleotide sequence distal to the rRNA operon from maize chloroplasts has been analyzed. It contains genes coding for tRNA(Arg)(ACG) and tRNA(Asn)(GUU). The tRNA(Arg)(ACG) gene, which is separated from the last rRNA gene of the rRNA operon, the 5S rDNA, by an intergenic region of 252 bp, has the same orientation a...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00020326
更新日期：1986-11-01 00:00:00
abstract：:The nuclear gene mutant of barley, vir-115, shows a developmentally induced loss of D1 synthesis that results in inactivation of Photosystem II. Translation in plastids isolated from 1 h illuminated vir-115 seedlings is similar to wild type. In wild-type barley, illumination of plants for 16 to 72 h results in increas...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00043874
更新日期：1994-06-01 00:00:00
abstract：:The LfKCS45 gene with a high sequence similarity to known 3-ketoacyl-CoA synthases of the membrane-bound fatty acid elongase was isolated from Lesquerella fendleri. The LfKCS45 gene has a 1464 bp open reading frame without introns, and is predicted to encode a polypeptide of 487 amino acids with an estimated molecular...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-004-6235-z
更新日期：2004-12-01 00:00:00
abstract：:Isolation of cDNAs encoding individual members of a gene family is essential for assessing their role in a biological phenomenon. However, this process is often laborious and slow due to highly conserved protein-coding region that interferes with the isolation of the individual members. Identification of gene-specific...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00042230
更新日期：1996-06-01 00:00:00
abstract：:A cDNA subtraction and differential hybridization strategy was used to isolate cDNAs expressed early during male gametophyte development in the important crop species Brassica napus. Three cDNAs, corresponding to genes highly and specifically expressed at the tetrad and microspore stages, are presented here. The analy...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1023/a:1006282507095
更新日期：1999-07-01 00:00:00
abstract：:We have cloned and sequenced a full-length cDNA from barley (Hordeum vulgare L.) seeds encoding the bifunctional α-amylase/subtilisin inhibitor (BASI). The nucleotide sequence predicts an open reading frame coding for a protein of 203 amino acids. The first 22 amino acids exhibit the sequence characteristic of a signa...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00044158
更新日期：1989-06-01 00:00:00
abstract：:We have cloned and sequenced a gene, pds, from the cyanobacterium Synechococcus PCC7942 that is responsible for resistance to the bleaching herbicide norflurazon. A point mutation in that gene, leading to an amino acid substitution from valine to glycine in its polypeptide product, was found to confer this resistance....
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00016069
更新日期：1991-06-01 00:00:00
abstract：KEY MESSAGE:Plant bioregulators play an important role in managing oxidative stress tolerance in plants. Utilizing their ability in stress sensitive crops through genetic engineering will be a meaningful approach to manage food production under the threat of climate change. Exploitation of the plant defense system agai...
journal_title：Plant molecular biology
pub_type： 杂志文章,评审
doi：10.1007/s11103-020-01077-w
更新日期：2021-01-01 00:00:00
abstract：KEY MESSAGE:OsWRKY36 represses plant height and grain size by inhibiting gibberellin signaling. Plant height and grain size are important agronomic traits affecting yield in cereals, including rice. Gibberellins (GAs) are plant hormones that promote plant growth and developmental processions such as stem elongation and...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-020-01049-0
更新日期：2020-11-01 00:00:00
abstract：:A cDNA encoding CYP79B1 has been isolated from Sinapis alba. CYP79B1 from S. alba shows 54% sequence identity and 73% similarity to sorghum CYP79A1 and 95% sequence identity to the Arabidopsis T42902, assigned CYP79B2. The high identity and similarity to sorghum CYP79A1, which catalyses the conversion of tyrosine to p...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1023/a:1006064202774
更新日期：1998-11-01 00:00:00
abstract：:When subjected to salt stress or drought, some vascular plants such as barley respond with an increased accumulation of the osmoprotectant glycine betaine (betaine), being the last step of betaine synthesis catalyzed by betaine aldehyde dehydrogenase (BADH). We report here cloning and characterization of BADH cDNA fro...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00020185
更新日期：1995-01-01 00:00:00
abstract：:The effect of red light and far-red light on the appearance of mRNA for the small and large subunit of ribulose-1,5-bisphosphate carboxylase in rye seedlings has been analysed. Irradiation of etiolated seedlings with a pulse of red light increased the mRNA level of the small subunit by a factor of 7-10 and that of the...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00014183
更新日期：1987-01-01 00:00:00
abstract：:Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication. A calcium phosphate-DNA mediated transformation procedure was employed in combination with either polyethylene glycol or polyvinyl alcohol. There were no indications ...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00015816
更新日期：1987-09-01 00:00:00
abstract：:Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Ch...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-011-9849-y
更新日期：2012-01-01 00:00:00
abstract：:A novel rice genomic sequence encoding coding segments homologous to other metallothionein-like genes was isolated from Oryza sativa genomic library. This sequence, hereby designated as rgMT (rice genomic metallothionein-like gene), consists of two exons and one intron. From the coding sequence, it is predicted that r...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00020388
更新日期：1995-06-01 00:00:00
abstract：:In wild-type Arabidopsis seeds the 2S albumin seed protein gene family members are differentially expressed. In this work it is shown that as predicted by the wild type situation, the at2S2 promoter is much more effective than that of the at2S1 gene in the expression of a transgene. However, unexpectedly high expressi...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00028867
更新日期：1994-11-01 00:00:00
abstract：:We studied the expression of the oat globulin gene asglo5 in developing transgenic tobacco seeds. The asglo5 gene promoter directed transcription in the endosperm as well as in the provascular tissue, the presumptive root tip and the shoot apical meristem of the embryo as revealed by GUS reporter gene constructs and i...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00039532
更新日期：1994-10-01 00:00:00
abstract：:A cDNA containing the entire coding region for the iron storage protein ferritin has been isolated from the French bean plant, Phaseolus vulgaris L. cv. Tendergreen. Ferritin protein was purified from young leaves and shoot meristem tissue and used to raise antisera in mice. A lambda gt11 cDNA library was constructed ...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/BF00040644
更新日期：1991-09-01 00:00:00
abstract：:Plant microRNAs (miRNAs) act as negative regulators of gene expression by slicing target transcripts or inhibiting translation. A number of miRNAs play important roles in development. In order to investigate the potential function of miRNAs during male gametogenesis in rice, we obtained both gene and small RNA express...
journal_title：Plant molecular biology
pub_type： 杂志文章
doi：10.1007/s11103-012-9898-x
更新日期：2012-09-01 00:00:00
