{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T18:48:57Z","timestamp":1768589337919,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,8,7]],"date-time":"2025-08-07T00:00:00Z","timestamp":1754524800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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,\u00a0the 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 \u201cCell Markers\u201d, \u201cSubtype Markers\u201d, and \u201cTPN Markers\u201d, 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\/.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf066","type":"journal-article","created":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T19:34:11Z","timestamp":1755027251000},"source":"Crossref","is-referenced-by-count":1,"title":["PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-5744-063X","authenticated-orcid":false,"suffix":"(\u5b5f\u4f73\u73a5)","given":"Jiayue","family":"Meng","sequence":"first","affiliation":[{"name":"National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences , Shanghai 200031,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3751-3219","authenticated-orcid":false,"suffix":"(\u97e9\u68a6\u7476)","given":"Mengyao","family":"Han","sequence":"additional","affiliation":[{"name":"Putuo People\u2019s Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University , Shanghai 200092,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1571-7103","authenticated-orcid":false,"suffix":"(\u9ec4\u4fde\u73ae)","given":"Yuwei","family":"Huang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences , Shanghai 200031,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2903-2347","authenticated-orcid":false,"suffix":"(\u674e\u6881)","given":"Liang","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences , Shanghai 200031,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2812-0657","authenticated-orcid":false,"suffix":"(\u97a0\u5143\u864e)","given":"Yuanhu","family":"Ju","sequence":"additional","affiliation":[{"name":"Shanghai Southgene Technology Co ., Ltd., Shanghai 201203,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5678-2486","authenticated-orcid":false,"suffix":"(\u5415\u5927\u5e86)","given":"Daqing","family":"Lv","sequence":"additional","affiliation":[{"name":"Shanghai Southgene Technology Co ., Ltd., Shanghai 201203,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0349-1890","authenticated-orcid":false,"suffix":"(\u9648\u6653\u71a0)","given":"Xiaoyi","family":"Chen","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences , Ningbo 315000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9122-6782","authenticated-orcid":false,"suffix":"(\u8881\u529b\u8d5f)","given":"Liyun","family":"Yuan","sequence":"additional","affiliation":[{"name":"National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences , Shanghai 200031,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8827-7546","authenticated-orcid":false,"suffix":"(\u5f20\u56fd\u5e86)","given":"Guoqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences , Shanghai 200031,","place":["China"]},{"name":"Shanghai Sixth People\u2019s Hospital , Shanghai 200233,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,7]]},"reference":[{"key":"2025102919270481300_qzaf066-B1","first-page":"12","article-title":"Cancer statistics, 2024","volume":"74","author":"Siegel","year":"2024","journal-title":"CA Cancer J Clin"},{"key":"2025102919270481300_qzaf066-B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13073-022-01050-w","article-title":"Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response","volume":"14","author":"Zhang","year":"2022","journal-title":"Genome Med"},{"key":"2025102919270481300_qzaf066-B3","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41568-018-0006-7","article-title":"A history of exploring cancer in context","volume":"18","author":"Maman","year":"2018","journal-title":"Nat Rev Cancer"},{"key":"2025102919270481300_qzaf066-B4","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1016\/j.molcel.2015.05.005","article-title":"Advances and applications of single-cell sequencing technologies","volume":"58","author":"Wang","year":"2015","journal-title":"Mol 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