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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 阮雪芬 | zh_TW |
| dc.contributor.advisor | Hsueh-Fen Juan | en |
| dc.contributor.author | 陳凱普 | zh_TW |
| dc.contributor.author | Kai-Pu Chen | en |
| dc.date.accessioned | 2023-07-19T16:46:21Z | - |
| dc.date.available | 2023-11-09 | - |
| dc.date.copyright | 2023-07-19 | - |
| dc.date.issued | 2023 | - |
| dc.date.submitted | 2023-03-24 | - |
| dc.identifier.citation | Ai, D., Pan, H., Li, X., Gao, Y., Liu, G. and Xia, L.C. (2019) Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model. Front Microbiol, 10, 826.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/87836 | - |
| dc.description.abstract | 微生物族群大量存在於人體內，而微生物失衡被報導與許多疾病相關，包括各種癌症。大多數研究都聚焦在腸道微生物菌相上，而參與腫瘤微環境中之細菌仍舊不太清楚。先前的研究已經從癌症基因組圖譜 (TCGA) 之核糖核酸定序、全基因組定序和全外顯子定序中獲得了細菌表達之資訊。卻很少使用微小核糖核酸定序之資料。我們的先導研究發現，使用 TCGA 微小核糖核酸定序資料發現大腸直腸癌 (CRC) 微生物與 16S 核糖體去氧核醣核酸定序技術中發現之微生物組相似。在本研究中，我們使用 TCGA 微小核糖核酸定序資料評估了 32 種癌症中之細菌相對表現量。為了發現與癌症關聯之細菌，我們使用了一種分析方法將未對應上人類之定序片段與細菌參考進行比對，並建立了 BIC 資料庫網站—癌症中細菌轉錄圖譜之資料庫。 BIC 提供與癌症相關之細菌資訊，包含細菌相對表現量、細菌多樣性、與臨床指標關聯性、細菌間、細菌和人類基因間之共表現網絡及其相關之生物功能性。這些結果可以互補先前已發表之資料庫。使用者可以輕鬆下載輸出結果之圖、表，或下載細菌相對表現量之矩陣做更進一步之分析。總而言之， BIC 可以提供腫瘤微環境中細菌相關之資訊。 BIC 可在下方網址中獲得：http://bic.jhlab.tw/。 | zh_TW |
| dc.description.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. Our pilot study found that the colorectal cancer (CRC) microbiome discovered with TCGA micro-RNA sequencing data is similar to those found in the 16S-rDNA sequencing technique. Using TCGA miRNA-Seq, we evaluated bacterial abundance in 32 types of cancer in this study. To uncover the bacteria involved in cancer, we applied an analytical process to align unmapped human reads to bacterial references and developed the bacteria in cancer (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/. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-07-19T16:46:20Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2023-07-19T16:46:21Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
致謝 ii 中文摘要 iii Abstract iv Contents v List of Figures ix List of Tables x Chapter 1 Introduction 1 1.1 Microbiota 1 1.2 Human microbiome 2 1.3 Microbial dysbiosis 2 1.4 Cancer microbiome 2 1.5 Regulatory work of small RNAs in bacteria 3 1.6 Polyadenylation in bacteria 3 1.7 The Cancer Genome Atlas (TCGA) 4 1.8 Related cancer microbiome studies using TCGA data 5 1.9 Motivation 5 Chapter 2 Materials and methods 6 2.1 Data collection 6 2.1.1 TCGA miRNA-Seq data 6 2.1.2 Human RNA expression profiles and clinical features 6 2.1.3 Gene sets 7 2.1.4 Retrieval of the biospecimen information 7 2.1.5 Microbial expression and metadata of the Cancer Microbiome Data Browser and TCMA databases 7 2.2 Processing from reads to bacterial expression 7 2.3 Filtering of samples 8 2.4 Bacterial expression matrices 8 2.4.1 GMPR normalization 8 2.4.2 Bacterial relative abundance matrices 8 2.5 Diversity 9 2.5.1 Richness (R) 9 2.5.2 Shannon index (H) 9 2.5.3 Gini-Simpson index 9 2.5.4 Inverse Simpson index 9 2.5.5 Shannon evenness index (SEI) 9 2.6 Composition 10 2.7 Clinical relevance 10 2.7.1 Survival test 10 2.7.2 Compare the bacterial relative abundance in different groups 10 2.8 Bacterial co-abundance 11 2.9 Co-expression of bacteria and human genes 11 2.10 Bacteria-associated biological functions 11 2.11 BIC database 11 2.11.1 BIC development 11 2.11.2 Data tables saved in PostgreSQL 12 2.11.3 BIC deployment 12 2.12 Comparison of Cancer Microbiome Data Browser, TCMA and BIC 13 Chapter 3 Results 14 3.1 Check for replicate sample 14 3.2 Summary of the processed data in BIC 14 3.3 Overview of BIC DB 14 3.4 Modules of analyses 15 3.4.1 Bacterial abundance 15 3.4.2 Bacterial diversity 15 3.4.3 Bacterial composition 16 3.4.4 Clinical relevance 17 3.4.5 Bacterial co-abundance network 18 3.4.6 Bacteria-human gene network 19 3.4.7 Bacteria-associated biological function 20 3.5 Other BIC webpages 21 3.6 Data availability and used software 22 3.7 Comparison between the database of the Cancer Microbiome Data Browser, TCMA and BIC 22 Chapter 4 Discussion 23 Chapter 5 Conclusion 25 References 26 | - |
| dc.language.iso | en | - |
| dc.subject | 細菌 | zh_TW |
| dc.subject | 微小核糖核酸定序資料 | zh_TW |
| dc.subject | 癌症基因組圖譜 | zh_TW |
| dc.subject | 癌症 | zh_TW |
| dc.subject | 癌症中細菌轉錄圖譜之資料庫 | zh_TW |
| dc.subject | Cancer | en |
| dc.subject | miRNA-Seq data | en |
| dc.subject | TCGA | en |
| dc.subject | Bacteria | en |
| dc.subject | BIC database | en |
| dc.title | 癌症中細菌轉錄圖譜之資料庫 | zh_TW |
| dc.title | BIC: a database for the transcriptional landscape of bacteria in cancer | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 111-2 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.coadvisor | 歐陽彥正 | zh_TW |
| dc.contributor.coadvisor | Yen-Jen Oyang | en |
| dc.contributor.oralexamcommittee | 黃宣誠;魏安祺;許家郎 | zh_TW |
| dc.contributor.oralexamcommittee | Hsuan-Cheng Huang;An-Chi Wei;Chia-Lang Hsu | en |
| dc.subject.keyword | 癌症,細菌,癌症基因組圖譜,微小核糖核酸定序資料,癌症中細菌轉錄圖譜之資料庫, | zh_TW |
| dc.subject.keyword | Cancer,Bacteria,TCGA,miRNA-Seq data,BIC database, | en |
| dc.relation.page | 67 | - |
| dc.identifier.doi | 10.6342/NTU202300685 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2023-03-25 | - |
| dc.contributor.author-college | 電機資訊學院 | - |
| dc.contributor.author-dept | 生醫電子與資訊學研究所 | - |
| 顯示於系所單位： | 生醫電子與資訊學研究所 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-111-2.pdf 授權僅限NTU校內IP使用（校園外請利用VPN校外連線服務） | 10.52 MB | Adobe PDF |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。