Evidence map›Paper›PMID 40795159›Full record

ArticleGenomics, proteomics & bioinformatics2025

PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation.

Jiayue Meng, Mengyao Han, Yuwei Huang, Liang Li, Yuanhu Ju, Daqing Lv, Xiaoyi Chen, Liyun Yuan, Guoqing Zhang

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PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, proteomics & bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
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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

9 authors.

Jiayue MengNational Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0009-0003-5744-063X
Mengyao HanPutuo People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.ORCID 0000-0002-3751-3219
Yuwei HuangNational Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0000-0003-1571-7103
Liang LiNational Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0009-0007-2903-2347
Yuanhu JuShanghai Southgene Technology Co., Ltd., Shanghai 201203, China.ORCID 0009-0009-2812-0657
Daqing LvShanghai Southgene Technology Co., Ltd., Shanghai 201203, China.ORCID 0009-0003-5678-2486
Xiaoyi ChenNingbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China.ORCID 0009-0005-0349-1890
Liyun YuanNational Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0000-0001-9122-6782
Guoqing ZhangNational Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0000-0001-8827-7546

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Research on cell type markers helps investigators explore the diverse cellular composition of gastrointestinal tumors, thereby enhancing our understanding of tumor heterogeneity and its impact on disease progression and treatment response. However, the integration of large-scale datasets and the standardization of cell type identification remain challenging. Here, we developed PreDigs, a user-friendly database of predicted signatures for the digestive system, which offers 124 curated single-cell RNA sequencing datasets, covering over 3.4 million cells, all available for download. After unsupervised clustering, we unified the identification and nomenclature of cell subtype labels, constructing a cell ontology tree with 142 cell types across 8 hierarchical levels. Meanwhile, we calculated three different context-specific cell type markers, including "Cell Markers", "Subtype Markers", and "TPN Markers", based on various application requirements within or across tissues. Through the integrated analysis of PreDigs data, we identified distinct cell subpopulations exclusive to tumors, one of which corresponds to tumor-specific endothelial cells. Additionally, PreDigs offers online cell annotation tools, allowing users to classify single cells with greater flexibility. PreDigs is accessible at https://www.biosino.org/predigs/.

Indexed as

Biomarkers, TumorDatabases, GeneticGastrointestinal NeoplasmsHumansSingle-Cell AnalysisSoftwareBiomarkers, TumorCell type markerDatabaseData integrationGastrointestinal tumorSingle-cell RNA sequencing

Identifiers

PMID40795159
PMCPMC12571502

What Socratic holds

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LicenceCC BY
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Registered trials

None linked

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 Socratic graph.