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研究生： 劉佳媛
Chia-Yuan Liu
論文名稱： 基因表現與乳癌亞型的關聯性分析
Association analysis of gene expression with breast cancer subtype
指導教授： 許藝瓊
Yi-Chiung Hsu
口試委員:
學位類別： 碩士
Master
系所名稱： 生醫理工學院 - 生醫科學與工程學系
Department of Biomedical Sciences and Engineering
論文出版年： 2025
畢業學年度： 113
語文別： 中文
論文頁數： 68
中文關鍵詞： 乳癌 、亞型 、高表達基因 、TCGA 、UALCAN
外文關鍵詞： Breast cancer, Subtypes, Gene expression, TCGA, UALCAN
相關次數： 點閱：28  下載：0 
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    • 乳癌是女性最常見的癌症，對全球健康構成重大威脅。隨著次世代基因定
    序（NGS，next generation sequencing）的快速發展，我們得以更深入地研究與乳癌相關的基因。特定基因的異常表達與乳癌的發展和預後息息相關。乳癌具有異質性，包含多種不同的亞型，每種亞型在基因表達、生物學特性和對治療的反應上都存在顯著差異。因此，在乳癌研究中考慮亞型因素至關重要，有助於更精準地理解不同亞型的發病機制和尋找更有效的治療策略。
    癌症基因組圖譜（TCGA）大型基因組計畫為研究這些基因提供了大量且完整的數據資源，能以系統性地分析大量乳癌樣本的基因。不僅有助於我們更深入地了解乳癌的分子機制，還能為開發更有效的標靶治療策略奠定基礎。標靶治療通過精準鎖定癌細胞中的特定基因，達到抑制腫瘤生長、擴散的目的，從而提高治療效果並降低副作用。更重要的是，發現新的標靶可以為那些對現有治療方法產生抗藥性的患者提供新的治療選擇，並有助於開發更個性化的治療方案。
    本篇在利用 UALCAN 平台和 TCGA 數據庫。UALCAN 平台支持基於轉錄組數據的基因表達量分析和 Kaplan-Meier 存活曲線生成，能夠快速篩選出在腫瘤組織中表達量顯著高於正常組織的基因。本篇的研究方法包括基因表達分析和存活分析，在分析特定高表達基因在乳癌中的角色，並探討這些基因與患者預後之間的關聯，同時考慮乳癌亞型的影響，以及快速地發現新的診斷標誌物和標靶治療，通過深入研究這些基因從而改善乳癌患者的預後，並為克服現有治療的局限性提供新的機會。最終為乳癌的早期診斷、精準治療和預後改善做出貢獻。

    Breast cancer is the most common cancer among women and poses a significant global health threat. As Next generation sequencing (NGS)improves by leaps and bounds, researchers are now able to gain deeper insights into genes associated with breast cancer. Abnormal expression of specific genes is closely linked to the development and prognosis of the disease. Breast cancer is a heterogeneous disease composed of multiple subtypes, each characterized by distinct gene expression patterns, biological behaviors, and treatment responses. Therefore, considering breast cancer subtypes is crucial for accurately understanding tumorigenesis and for
    identifying more effective therapeutic strategies.The Cancer Genome Atlas (TCGA), a large-scale genomics initiative, offers a comprehensive dataset that enables systematic
    analysis of gene expression across numerous breast cancer samples. This resource not only enhances our understanding of the molecular mechanisms of breast cancer but also lays the foundation for the development of more effective targeted therapies. Targeted therapies work by precisely inhibiting specific genes in cancer cells to suppress tumor growth and metastasis, thereby improving treatment outcomes and minimizing side effects. Moreover, the discovery of novel targets may offer alternative treatment options for patients who develop resistance to existing therapies,
    and it facilitates the advancement of personalized medicine.In this study, we utilized the UALCAN platform and TCGA database. UALCAN supports transcriptome-based
    gene expression analysis and Kaplan–Meier survival curve enabling rapid identification of genes that are significantly overexpressed in tumor tissues compared
    to normal tissues. The research methodology includes gene expression analysis and survival analysis to investigate the role of specific highly expressed genes in breast cancer, examine their association with patient prognosis, and assess the impact of molecular subtypes. The ultimate goal is to identify novel diagnostic biomarkers and therapeutic targets, improve patient outcomes, and provide new opportunities to overcome the limitations of current treatments—thereby contributing to early diagnosis, precision medicine, and enhanced prognosis in breast cancer.

    中文摘要 .............i Abstract .............. ii 致謝 ................... iii 目錄 .................... iv 圖目錄 .............. vii 表目錄 ................ x 一、 緒論 ....... 1 1-1 研究動機 ....... 1 1-2 研究背景 ............. 1 1-3 乳癌的基因表現與突變 ....... 2 1-4 TCGA（The Cancer Genome Atlas）...... 3 1-5 UALCAN ............ 3 1-6 差異表達基因（DEGs） ........ 4 二 、研究工具 .............. 5 2-1癌症基因組圖譜計畫(TheCancerGenomeAtlas,TCGA) .......... 5 2-2 UALCAN .............. 5 三 、研究方法 ............. 7 3-1數據採集 .............. 7 3-2存活分析 .............. 7 3-3分析流程 ............... 8 四 、結果 .................. 9 4-1 存活分析與基因表達 .............. 9 4-1-1存活分析與COL10A1基因表達 ..... 10 4-1-2存活分析與CST1基因表達................... 11 4-1-3存活分析與MMP11基因表達........ 12 4-1-4存活分析與NEK2基因表達 ........ 13 4-1-5存活分析與UBE2C基因表達 ....... 14 4-1-6存活分析與NUF2基因表達 ......... 15 4-1-7存活分析與CXCL10基因表達 ....... 16 4-1-8存活分析與PBK基因表達 ........ 17 4-1-9存活分析與AURKB基因表達 ........ 18 4-1-10存活分析與CEP55基因表達 ...... 19 4-1-11存活分析與ANLN基因表達 ........ 20 4-2 表達量分析 ................ 21 4-2-1 COL10A1 在乳癌中的表達 ......... 22 4-2-2 CST1在乳癌中的表達 ........ 23 4-2-3 MMP11在乳癌中的表達 ....... 24 4-2-4 NEK2在乳癌中的表達 ........ 25 4-2-5 UBE2C在乳癌中的表達 ......... 26 4-2-6 NUF2在乳癌中的表達 ............ 27 4-2-7 CXCL10在乳癌中的表達 ....... 28 4-2-8 PBK在乳癌中的表達 .......... 29 4-2-9 AURKB在乳癌中的表達 ............... 30 4-2-10 CEP55在乳癌中的表達 ............ 31 4-2-11 ANLN在乳癌中的表達........... 32 4-3與 TP53 突變狀態的關聯性 .......... 33 4-3-1 COL10A1與 TP53 突變狀態的關聯性 ................. 34 4-3-2 CST1與 TP53 突變狀態的關聯性 ........ 34 4-3-3 MMP11與 TP53 突變狀態的關聯性 .... 35 4-3-4 NEK2與 TP53 突變狀態的關聯性 ........ 35 4-3-5 UBE2C與 TP53 突變狀態的關聯性 ..... 36 4-3-6 NUF2與 TP53 突變狀態的關聯性 ...... 36 4-3-7 CXCL10與 TP53 突變狀態的關聯性 .... 37 4-3-8 PBK與 TP53 突變狀態的關聯性 ......... 37 4-3-9 AURKB與 TP53 突變狀態的關聯性 ..... 38 4-3-10 CEP55與 TP53 突變狀態的關聯性 ..... 38 4-3-11 ANLN與 TP53 突變狀態的關聯性 ..... 39 4-4 文獻探討 .................... 40 4-4-1 COL10A1 ................... 40 4-4-2 CST1 ..................... 41 4-4-3 MMP11 ........... 41 4-4-4 NEK2 .................... 42 4-4-5 UBE2C ......... 42 4-4-6 NUF2 ........... 43 4-4-7 CXCL10................... 43 4-4-8 PBK ................ 44 4-4-9 AURKB ............... 44 4-4-10 CEP55 ................... 45 4-4-11 ANLN ...................... 45 五 、總結 ..... 47 六 、未來工作 ................. 48 七 、參考文獻 ......................... 49 圖目錄 圖 1 流程圖 ........................ 7 圖 2分析流程 ............... 8 圖 3 . COL10A1表達對乳癌患者生存的影響 .................... 10 圖 4 . COL10A1表達和癌症分型對乳癌患者生存的影響 ........... 10 圖 5 . CST1表達對乳癌患者生存的影響 ............... 11 圖 6 .CST1表達和癌症分型對乳癌患者生存的影響 ........... 11 圖 7 . MMP11表達對乳癌患者生存的影響 ............. 12 圖 8 . MMP11表達和癌症分型對乳癌患者生存的影響 .......... 12 圖 9 . NEK2表達對乳癌患者生存的影響 ......... 13 圖 10 . NEK2表達和癌症分型對乳癌患生存的影響 ........ 13 圖 11 . UBE2C表達對乳癌患者生存的影響 ............ 14 圖 12 . UBE2C表達和癌症分型對乳癌患者生存的影響 ...... 14 圖 13. NUF2表達對乳癌患者生存的影響 ................. 15 圖 14 . NUF2表達和癌症分型對乳癌患者生存的影響 ..... 15 圖 15. CXCL10表達對乳癌患者生存的影響 ... 16 圖 16 .CXCL10 表達和癌症分型對乳癌患者生存的影響 .......... 16 圖 17. PBK 表達對乳癌患者生存的影響 ........... 17 圖 18. PBK 表達和癌症分型對乳癌患者生存的影響 ...... 17 圖 19. AURKB 表達對乳癌患者生存的影響 ........ 18 圖 20. AURKB表達和癌症分型對乳癌患者生存的影響 ........ 18 圖 21. CEP55 表達對乳癌患者生存的影響 ........... 19 圖 22. CEP55表達和癌症分型對乳癌患者生存的影響 ............ 19 圖 23. ANLN表達對乳癌患者生存的影響 .................... 20 圖 24. ANLN表達和癌症分型對乳癌患患者生存的影響 ............ 20 圖 25.正常組織vs.癌組織COL10A1基因表達量 ......... 22 圖 26.不同乳癌亞型COL10A1基因表達量.................... 22 圖 27.正常組織vs.癌組織CST1基因表達量 .................. 23 圖 28.不同乳癌亞型CST1基因表達量 ...................... 23 圖 29.正常組織vs.癌組織MMP11基因表達量 ................. 24 圖30.不同乳癌亞型MMP11基因表達量 ......................... 24 圖 31.正常組織vs.癌組織NEK2基因表達量差異 ........... 25 圖 32.不同乳癌亞型NEK2基因表達量差異 ............... 25 圖 33.正常組織vs.癌組織UBE2C基因表達量差異 ......... 26 圖 34.不同乳癌亞型UBE2C基因表達量差異 ..... 26 圖 35.正常組織vs.癌組織NUF2基因表達量差異 ......... 27 圖 36.不同乳癌亞型NUF2基因表達量差異 ....27 圖 37.正常組織vs.癌組織CXCL10基因表達量差異 .... 28 圖 38.不同乳癌亞型CXCL10基因表達量差異 ........ 28 圖 39.正常組織vs.癌組織PBK基因表達量差異 ......... 29 圖 40.不同乳癌亞型PBK基因表達量差異 ................. 29 圖 41.正常組織vs.癌組織AURKB基因表達量差異 ....... 30 圖 42.不同乳癌亞型AURKB基因表達量差異 .......... 30 圖 43.正常組織vs.癌組織CEP55基因表達量 ............ 31 圖 44.不同乳癌亞型CEP55基因表達量差異 .......... 31 圖 45.正常組織vs.癌組織ANLN基因表達量 .......... 32 圖 46.不同乳癌亞型ANLN基因表達量差異 ......... 32 圖 47 .COL10A1與 TP53 突變狀態的關聯性 ......... 34 圖 48 .CST1與 TP53 突變狀態的關聯性 ................... 34 圖 49. MMP11與 TP53 突變狀態的關聯性 ........... 35 圖 50. NEK2與 TP53 突變狀態的關聯性........... 35 圖 51. UBE2C與 TP53 突變狀態的關聯性............ 36 圖 52. NUF2與 TP53 突變狀態的關聯性............. 36 圖 53. CXCL10與 TP53 突變狀態的關聯性......... 37 圖 54. PBK與 TP53 突變狀態的關聯性............ 37 圖 55. AURKB與 TP53 突變狀態的關聯性...... 38 圖 56. CEP55與 TP53 突變狀態的關聯性........... 38 圖 57. ANLN與 TP53 突變狀態的關聯性............ 39 表目錄 表 1乳癌分型......... 1 表 2 MeanTumorTPM/MeanNormalTPM>10且生存分析表現顯著(P<0.05)的11個基因........ 9 表 3 COL10A1基在正常組織與乳癌腫瘤中表現統計值 ....... 22 表 4 COL10A1基因在乳癌不同亞型與正常組組織與乳癌腫瘤中表現統計值 ... 22 表 5 CST1基因在正常組織與乳癌腫瘤中表現統計值 ........ 23 表 6 CST1基因在乳癌不同亞型與正常組織與乳癌腫瘤中表現統計值 .............. 23 表 7 MMP11基因在正常組織與乳癌腫瘤中表現統計值 .......... 24 表 8 MMP11基因在乳癌不同亞型與正常組織與乳癌腫瘤中表現統計值 .......... 24 表 9 NEK2基因在正常組織與乳癌腫瘤中表現統計值 ........... 25 表 10 NEK2基因在乳癌不同亞型與正常組織與乳癌腫瘤中表現統計值 ........... 25 表 11 UBE2C基因在正常組織與乳癌腫瘤中表現統計值 ......... 26 表 12 UBE2C基因在乳癌不同亞型與正常組織與乳癌腫瘤中表現統計值 ......... 26 表 13 NUF2 基因在正常組織與乳癌腫瘤中表現統計值...27 表 14NUF2 基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值................ 27 表 15 CXCL10基因在正常組織與乳癌腫瘤中表現統計值 ... 28 表 16 CXCL10 基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值 .......... 28 表 17 PBK基因在正常組織與乳癌腫瘤中表現統計值 ...... 29 表 18 PBK 基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值 ................. 29 表 19 AURKB基因在正常組織與乳癌腫瘤中表現統計值 ...... 30 表 20 AURKB基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值 ............ 30 表 21 CEP55基因在正常組織與乳癌腫瘤中表現統計值 ..... 31 表 22 CEP55基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值 .............. 31 表 23 ANLN基因在正常組織與乳癌腫瘤中表現統計值 .... 32 表 24 ANLN基因在乳癌不同亞型正常組織與乳癌腫瘤中表現統計值 ............... 32 表 25依據 TP53 突變狀態的 COL10A1基因在乳癌中的表現 ..... 34 表 26 依據 TP53 突變狀態的 CST1 基因在乳癌中的表現......... 34 表 27依據 TP53 突變狀態的MMP11基因在乳癌中的表現 ....... 35 表 28 依據 TP53 突變狀態的NEK2基因在乳癌中的表現 ........ 35 表 29依據 TP53 突變狀態的UBE2C基因在乳癌中的表現 ....... 36 表 30 依據 TP53 突變狀態的NUF2基因在乳癌中的表現 ...... 36 表 31 依據 TP53 突變狀態的CXCL10基因在乳癌中的表現 ..... 37 表 32依據 TP53 突變狀態的PBK基因在乳癌中的表現 ........ 37 表 33 依據 TP53 突變狀態的AURKB基因在乳癌中的表現 ...... 38 表 34依據 TP53 突變狀態的CEP55基因在乳癌中的表現...... 38 表 35 依據 TP53 突變狀態的ANLN基因在乳癌中的表現 ....... 39

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