Evidence map›Paper›PMID 41257542›Full record

ArticleBMC genomics2025

AmDB: functional genomics database of Astragalus membranaceus.

Hui Zhang, Dong Han, Jianqi Li, Jing Fang, Ying Zhang, Lujie Yang, Xinxin Zhang, Lina Zeng, Zhiqi Wang, Tingyu Li and 6 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

16 authors.

Hui Zhang *College of Life Science, Northwest Normal University, Lanzhou, China.
Dong Han *College of Life Science, Northwest Normal University, Lanzhou, China.
Jianqi LiCollege of Life Science, Northwest Normal University, Lanzhou, China.
Jing FangCollege of Life Science, Northwest Normal University, Lanzhou, China.
Ying ZhangCollege of Life Science, Northwest Normal University, Lanzhou, China.
Lujie YangCollege of Life Science, Northwest Normal University, Lanzhou, China.
Xinxin ZhangCollege of Life Science, Northwest Normal University, Lanzhou, China.
Lina ZengCollege of Life Science, Northwest Normal University, Lanzhou, China.
Zhiqi WangCollege of Life Science, Northwest Normal University, Lanzhou, China.
Tingyu LiCollege of Life Science, Northwest Normal University, Lanzhou, China.
Enguang ZhaoCollege of Life Science, Northwest Normal University, Lanzhou, China.
Jiande LiCollege of Life Science, Northwest Normal University, Lanzhou, China.
Junxia AnCollege of Life Science, Northwest Normal University, Lanzhou, China.
Qi YouKey Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China.
Yue LiuCollege of Horticulture, Qingdao Agricultural University, Qingdao, China.
Lingling DaCollege of Life Science, Northwest Normal University, Lanzhou, China. linglingda@nwnu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Astragalus membranaceus (A. membranaceus) belongs to the genus Astragalus within the family Leguminosae. Astragalus membranaceus var. mongholicus (A. mongholicus) is a variety of A. membranaceus. Its dried root is a Chinese herbal medicine, also known as "Huang Qi". Sequencing technology has made a large amount of high-quality transcriptomics data for A. mongholicus and A. membranaceus publicly available. Their whole genomes were sequenced in 2022 and 2024, respectively. Despite the increasing availability of genomic and transcriptomic data, a reliable platform for comparing and mining gene function information remains unavailable. To fill this gap, this study aimed to develop AmDB ( http://bioinformatics.nwnu.edu.cn/AmDB/ ), a functional genomics database of A. membranaceus. First, functional and structural annotations were performed for 27,245 genes based on genomic data, using algorithms and software tools. Second, 62 transcriptome samples were collected from the SRA database. A co-expression network was constructed using the Pearson correlation coefficient and the Mutual Rank method, containing 224,615 positive and 116,806 negative gene pairs, covering 94.87% of the coding genes. The network analysis revealed that the phenylalanine ammonia-lyase function was closely related to phenylpropanoid metabolism, and the positively co-expressed genes in the network exhibited similar expression patterns. These findings validated the reliability of the network. Finally, AmDB implemented easy-to-use bioinformatics tools, including gene set enrichment analysis, BLAST, sequence extraction, orthologue identification, JBrowse, and expression data extraction.

Indexed as

Astragalus propinquusDatabases, GeneticGenomicsComputational BiologyGene Expression ProfilingMolecular Sequence AnnotationTranscriptomeAstragalus membranaceusBioinformatics toolsCo-expression networkFunctional annotation

Identifiers

PMID41257542
PMCPMC12821240

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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.