ArticleNucleic acids research2023
BIC: a database for the transcriptional landscape of bacteria in cancer.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Bacterial-based cancer therapy: mechanisms and therapeutic advances.Molecular biomedicine · 2026Review
- Metabolome-microbiome convergence under circadian disruption accelerates mammary tumorigenesis: multi-omics integration insights.BMC cancer · 2026Article
- Enterococcus faecalis Extracellular Vesicles Deliver the Bacterial GTPase Obg to Hijack mTOR Signalling in Hepatocellular Carcinoma.Journal of extracellular vesicles · 2026Article
- Systematic evaluation of TCGA tumor microbiota reveals context-dependent reliability.mSystems · 2026Article
- SCMO: a deep learning model integrating the single-cell resolution TME ecosystem and multi-omics for survival prediction in CRC patients.Journal of translational medicine · 2026Article
- Gut microbiota centered approaches for breast cancer intervention leveraging probiotics and postbiotics.Discover oncology · 2026Review
- Tumor microbiome-transcriptome crosstalk identifiesTheranostics · 2026Article
- Intratumoral Microbiota Correlates with AP-2 Expression: A Pan-Cancer Map with Cohort-Specific Prognostic and Molecular Footprints.International journal of molecular sciences · 2025Article
- HGMT: a database of human gut microbiota for tumors and immunotherapy response.Genome biology · 2025Article
- SMTdb: A Comprehensive Spatial Meta-Transcriptome Resource in Cancer.Molecular biology and evolution · 2025Article
- Effect of immune-related intratumoral microbiota and host gene expression on cancer prognosis.mSystems · 2025Article
- Intratumoral core microbiota predicts prognosis and therapeutic response in gastrointestinal cancers.Microbiology spectrum · 2025Article
- An interpretable CT-based deep learning model for predicting overall survival in patients with bladder cancer: a multicenter study.NPJ precision oncology · 2025Article
- Article
- Intratumoral Brevibacillus parabrevis enhances antitumor immunity by inhibiting NK cell ferroptosis in hepatocellular carcinoma.Cell death & disease · 2025Article
- Fusobacterium nucleatum-Derived Outer Membrane Vesicles Promote Immunotherapy Resistance via Changes in Tryptophan Metabolism in Tumour-Associated Macrophages.Journal of extracellular vesicles · 2025Article
- Article
- Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma.Scientific reports · 2025Article
- Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.Journal of translational medicine · 2025Article
- Deciphering the impact of intra-tumoral bacterial infiltration on multi-omics profiles in low-grade gliomas.Frontiers in oncology · 2025Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities are massively resident in the human body, yet dysbiosis has been reported to correlate with many diseases, including various cancers. Most studies focus on the gut microbiome, while the bacteria that participate in tumor microenvironments on site remain unclear. Previous studies have acquired the bacteria expression profiles from RNA-seq, whole genome sequencing, and whole exon sequencing in The Cancer Genome Atlas (TCGA). However, small-RNA sequencing data were rarely used. Using TCGA miRNA sequencing data, we evaluated bacterial abundance in 32 types of cancer. To uncover the bacteria involved in cancer, we applied an analytical process to align unmapped human reads to bacterial references and developed the BIC database for the transcriptional landscape of bacteria in cancer. BIC provides cancer-associated bacterial information, including the relative abundance of bacteria, bacterial diversity, associations with clinical relevance, the co-expression network of bacteria and human genes, and their associated biological functions. These results can complement previously published databases. Users can easily download the result plots and tables, or download the bacterial abundance matrix for further analyses. In summary, BIC can provide information on cancer microenvironments related to microbial communities. BIC is available at: http://bic.jhlab.tw/.
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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.