Evidence map›Paper›PMID 41092484›Full record

ArticleMolecular biology and evolution2025

SMTdb: A Comprehensive Spatial Meta-Transcriptome Resource in Cancer.

Weiwei Zhou, Qingyi Yang, Jiyu Guo, Si Li, Minghai Su, Feng Leng, Tingyu Rong, Jingyi Shi, Yueying Gao, Tiantongfei Jiang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular biology and evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

12 authors.

Weiwei ZhouCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0003-1641-8965
Qingyi YangSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0009-0000-6636-6628
Jiyu GuoSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0009-0000-0429-4833
Si LiSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0009-0009-1394-1540
Minghai SuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0001-5135-3103
Feng LengCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0009-0000-0249-3564
Tingyu RongSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0009-0006-3392-0876
Jingyi ShiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0009-0004-0214-0311
Yueying GaoSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0009-0003-3095-8228
Tiantongfei JiangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0009-0008-5376-7922
Juan XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0002-3709-4165
Yongsheng LiSchool of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China.ORCID 0000-0003-1914-0727

Funding

National Natural Science Foundation of China 32060152National Natural Science Foundation of China 32170676National Natural Science Foundation of China 32322020Natural Science Foundation of Heilongjiang Province ZD2023C007Noncommunicable Chronic Diseases-National Science and Technology Major 2024ZD0533300
6 · The paper itself

Abstract

Microorganisms have been detected in various tumors, and research on the tumor microbiome has received increasing attention. However, the investigation of the cancer microbiome at the spatial resolution level remains a challenging issue. The emergence of spatially resolved transcriptomics technology has enabled to map transcripts at the single-cell resolution in various cancer types. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen slices from 20 cancer types encompassing 334,253 spots and 1,908,646 cells. A spatial meta-transcriptome database (SMTdb; http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide detailed insights into the abundance, distribution, and enriched tumor microenvironment (TME) regions of 1,218 microbiota in spatial tissue slices. SMTdb enables to explore the vast interactive data of spatial distribution and expression of microbiota, provides host gene modules associated with certain microbiota, and contains data on the co-occurrence between the microbiota and immune cells within the TME. The atlas resource serves as a comprehensive and structured platform to investigate the interactions between microbial ecosystems and hosts in cancer.

Indexed as

Databases, GeneticMicrobiotaNeoplasmsTranscriptomeHumansTumor Microenvironmentdatabaseimmune cellsmicrobiotasingle-cell omicsspatially resolved transcriptomicstumor microenvironment

Identifiers

PMID41092484
PMCPMC12596269

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Registered trials

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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.