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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\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac891","type":"journal-article","created":{"date-parts":[[2022,10,20]],"date-time":"2022-10-20T10:02:15Z","timestamp":1666260135000},"page":"D1205-D1211","source":"Crossref","is-referenced-by-count":32,"title":["BIC: a database for the transcriptional landscape of bacteria in cancer"],"prefix":"10.1093","volume":"51","author":[{"given":"Kai-Pu","family":"Chen","sequence":"first","affiliation":[{"name":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , Taipei 106, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chia-Lang","family":"Hsu","sequence":"additional","affiliation":[{"name":"Department of Medical Research, National Taiwan University Hospital , Taipei 100, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yen-Jen","family":"Oyang","sequence":"additional","affiliation":[{"name":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , Taipei 106, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3386-0934","authenticated-orcid":false,"given":"Hsuan-Cheng","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Informatics, National Yang Ming Chiao Tung University , Taipei 112, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4876-3309","authenticated-orcid":false,"given":"Hsueh-Fen","family":"Juan","sequence":"additional","affiliation":[{"name":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , Taipei 106, Taiwan"},{"name":"Department of Life Science, National Taiwan University , Taipei 106, Taiwan"},{"name":"Center for Computational and Systems Biology, National Taiwan University , Taipei 106, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,20]]},"reference":[{"key":"2023010804225137000_B1","doi-asserted-by":"crossref","first-page":"1694","DOI":"10.1126\/science.1177486","article-title":"Bacterial community variation in human body habitats across space and time","volume":"326","author":"Costello","year":"2009","journal-title":"Science"},{"key":"2023010804225137000_B2","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrg3182","article-title":"The human microbiome: at the interface of health and disease","volume":"13","author":"Cho","year":"2012","journal-title":"Nat. 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