ArticleBMC genomics2025
Black pepper knowledge base (BlackPepKB): a centralized web resource for functional genomics of black pepper (Piper nigrum L.).
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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.
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.
Who cites it
1 citing paper in PubMed.
- Deciphering Stress Resilience in Black Pepper (International journal of molecular sciences · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBlack pepper (Piper nigrum L.) is a highly valued spice crop with significant economic, medicinal, and cultural importance. While genomic and transcriptomic data for black pepper have rapidly accumulated in recent years, there is currently no dedicated genomic database to serve as a centralized web resource for the research and breeding community. Furthermore, despite the availability of a reference genome, the functional annotation of its proteome and a comprehensive repertoire of its transcription factors (TFs) remain incomplete.
resultsWe identified a total of 2,503 TF-encoding genes in black pepper (PnTFs), classified into 62 TF families. Notably, 471 intronless PnTF genes were identified, with more than 50% of genes in families such as Dof, ERF, GeBP, GRAS, NF-YB, RAV, TCP, Trihelix, and ZF-HD, suggesting their potential roles in regulating stress responses. Protein-protein interaction network analysis identified 171 hub PnTFs that may serve as key regulators in diverse biological processes. In addition, Gene Ontology-based functional annotation of 63,463 proteins in black pepper revealed that 35,670 (56.2%) were annotated with at least one GO term. To support continued research and data exploration, we developed Black Pepper Knowledge Base (BlackPepKB), a user-friendly, integrative genomic platform for black pepper. BlackPepKB hosts genomic, transcriptomic, and functional annotation data, and incorporates interactive tools to enhance data accessibility. Key features include an electronic Fluorescent Pictograph (eFP) browser for visualizing gene expression patterns across tissues and developmental stages, JBrowse2 for genome navigation, BLAST for sequence similarity searches, and GeneViz for exon-intron gene structure visualization. Additionally, PepperExp and PepperClust tools enable heatmap generation and hierarchical clustering of gene expression data, while GO-Pep facilitates the retrieval of GO terms. The platform also offers user-friendly interfaces for querying single nucleotide polymorphisms and exploring TF families in black pepper.
conclusionBlackPepKB serves as the first dedicated genomic database for black pepper, providing a comprehensive and accessible platform for functional genomics research. This work lays a solid foundation for advancing genetic research and molecular breeding in black pepper. BlackPepKB is publicly accessible at: https://black-pepper-genomic-resource.vercel.app/ .
Indexed as
Identifiers
What OpenQuestion holds
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.