ArticleBMC bioinformatics2020
CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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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.
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Who cites it
7 citing papers in PubMed, 16 citations in OpenAlex.
- Genome-Wide Profiling of P450 Gene Expression Reveals Caste-Specific and Developmental Patterns inInternational journal of molecular sciences · 2025Article
- Detection of anaerobic and aerobic bacteria from commercial tattoo and permanent makeup inks.Applied and environmental microbiology · 2024Article
- Differential RNA-Seq Analysis Predicts Genes Related to Terpene Tailoring inPlants (Basel, Switzerland) · 2023Article
- Cytochromes P450 involved in bacterial RiPP biosyntheses.Journal of industrial microbiology & biotechnology · 2023Review
- Engineering medicinal plant-derived CYPs: a promising strategy for production of high-valued secondary metabolites.Planta · 2022Review
- The Transcription Factor CsAtf1 Negatively Regulates the Cytochrome P450 GeneJournal of fungi (Basel, Switzerland) · 2022Article
- Black fungi and ants: a genomic comparison of species inhabiting carton nests versus domatia.IMA fungus · 2022Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner.
resultsCYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences.
conclusionsCYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.
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Registered trials
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.