Evidence map›Paper›PMID 26055100›Full record

ArticleDatabase : the journal of biological databases and curation2015

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes.

Jaeyoung Choi, Ki-Tae Kim, Aram Huh, Seomun Kwon, Changyoung Hong, Fred O Asiegbu, Junhyun Jeon, Yong-Hwan Lee

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Databases and prospects of dynamic gene regulation in eukaryotes: A mini review.Computational and structural biotechnology journal · 2023
    Review
  5. MIAOME: Human microbiome affect the host epigenome.Computational and structural biotechnology journal · 2022
    Article
  6. Article
  7. Article
  8. Review
  9. Article
  10. Review
  11. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Jaeyoung ChoiDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Ki-Tae KimDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Aram HuhDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Seomun KwonDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Changyoung HongDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Fred O AsiegbuDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
Junhyun JeonDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea yonglee@snu.ac.kr.
Yong-Hwan LeeDepartment of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies.

Indexed as

Databases, ProteinEpigenesis, GeneticHistonesProteomeWeb BrowserAcetylationEpigenomicsMethylationProtein Processing, Post-TranslationalHistonesProteome

Identifiers

PMID26055100
PMCPMC4460409

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.