细胞特征与基因表达的CCA相关性研究

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摘要翻译：
为了理解癌症的生物学，包括成像和基因组学在内的多种数据模式的联合分析是至关重要的。基因与微环境相互作用的本质要求使用同等对待这两种数据类型的算法。我们建议使用典型相关分析(CCA)和稀疏变体作为一种初步发现工具来识别跨模式的联系，特别是在组织病理学图像中描述细胞和细胞核形状、纹理和染色强度的基因表达和特征之间的联系。应用于癌症基因组图谱中的615个乳腺癌样本，CCA揭示了几个图像特征与PAM50基因表达的显著相关性，已知这些基因与预后有关，而稀疏CCA揭示了与癌症相关的通路的富集相关，而没有利用先前的生物学理解。这些发现肯定了CCA在癌症联合表型-基因型分析中的效用。
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英文标题：
《Correlating Cellular Features with Gene Expression using CCA》
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作者：
Vaishnavi Subramanian, Benjamin Chidester, Jian Ma, Minh N. Do
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最新提交年份：
2018
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分类信息：

一级分类：Electrical Engineering and Systems Science        电气工程与系统科学
二级分类：Signal Processing        信号处理
分类描述：Theory, algorithms, performance analysis and applications of signal and data analysis, including physical modeling, processing, detection and parameter estimation, learning, mining, retrieval, and information extraction. The term "signal" includes speech, audio, sonar, radar, geophysical, physiological, (bio-) medical, image, video, and multimodal natural and man-made signals, including communication signals and data. Topics of interest include: statistical signal processing, spectral estimation and system identification; filter design, adaptive filtering / stochastic learning; (compressive) sampling, sensing, and transform-domain methods including fast algorithms; signal processing for machine learning and machine learning for signal processing applications; in-network and graph signal processing; convex and nonconvex optimization methods for signal processing applications; radar, sonar, and sensor array beamforming and direction finding; communications signal processing; low power, multi-core and system-on-chip signal processing; sensing, communication, analysis and optimization for cyber-physical systems such as power grids and the Internet of Things.
信号和数据分析的理论、算法、性能分析和应用，包括物理建模、处理、检测和参数估计、学习、挖掘、检索和信息提取。“信号”一词包括语音、音频、声纳、雷达、地球物理、生理、（生物）医学、图像、视频和多模态自然和人为信号，包括通信信号和数据。感兴趣的主题包括：统计信号处理、谱估计和系统辨识；滤波器设计；自适应滤波/随机学习；（压缩）采样、传感和变换域方法，包括快速算法；用于机器学习的信号处理和用于信号处理应用的机器学习；网络与图形信号处理；信号处理中的凸和非凸优化方法；雷达、声纳和传感器阵列波束形成和测向；通信信号处理；低功耗、多核、片上系统信号处理；信息物理系统的传感、通信、分析和优化，如电网和物联网。
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一级分类：Electrical Engineering and Systems Science        电气工程与系统科学
二级分类：Image and Video Processing        图像和视频处理
分类描述：Theory, algorithms, and architectures for the formation, capture, processing, communication, analysis, and display of images, video, and multidimensional signals in a wide variety of applications. Topics of interest include: mathematical, statistical, and perceptual image and video modeling and representation; linear and nonlinear filtering, de-blurring, enhancement, restoration, and reconstruction from degraded, low-resolution or tomographic data; lossless and lossy compression and coding; segmentation, alignment, and recognition; image rendering, visualization, and printing; computational imaging, including ultrasound, tomographic and magnetic resonance imaging; and image and video analysis, synthesis, storage, search and retrieval.
用于图像、视频和多维信号的形成、捕获、处理、通信、分析和显示的理论、算法和体系结构。感兴趣的主题包括：数学，统计，和感知图像和视频建模和表示；线性和非线性滤波、去模糊、增强、恢复和重建退化、低分辨率或层析数据；无损和有损压缩编码；分割、对齐和识别；图像渲染、可视化和打印；计算成像，包括超声、断层和磁共振成像；以及图像和视频的分析、合成、存储、搜索和检索。
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一级分类：Quantitative Biology        数量生物学
二级分类：Cell Behavior        细胞行为
分类描述：Cell-cell signaling and interaction; morphogenesis and development; apoptosis; bacterial conjugation; viral-host interaction; immunology
细胞-细胞信号传导及相互作用；形态发生和发育；细胞凋亡；细菌接合；病毒-宿主相互作用；免疫学
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一级分类：Quantitative Biology        数量生物学
二级分类：Quantitative Methods        定量方法
分类描述：All experimental, numerical, statistical and mathematical contributions of value to biology
对生物学价值的所有实验、数值、统计和数学贡献
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一级分类：Statistics        统计学
二级分类：Applications        应用程序
分类描述：Biology, Education, Epidemiology, Engineering, Environmental Sciences, Medical, Physical Sciences, Quality Control, Social Sciences
生物学，教育学，流行病学，工程学，环境科学，医学，物理科学，质量控制，社会科学
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英文摘要：
  To understand the biology of cancer, joint analysis of multiple data modalities, including imaging and genomics, is crucial. The involved nature of gene-microenvironment interactions necessitates the use of algorithms which treat both data types equally. We propose the use of canonical correlation analysis (CCA) and a sparse variant as a preliminary discovery tool for identifying connections across modalities, specifically between gene expression and features describing cell and nucleus shape, texture, and stain intensity in histopathological images. Applied to 615 breast cancer samples from The Cancer Genome Atlas, CCA revealed significant correlation of several image features with expression of PAM50 genes, known to be linked to outcome, while Sparse CCA revealed associations with enrichment of pathways implicated in cancer without leveraging prior biological understanding. These findings affirm the utility of CCA for joint phenotype-genotype analysis of cancer.
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PDF链接：
https://arxiv.org/pdf/1802.0891

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关键词：基因表达 相关性 Applications Quantitative Optimization 染色 615 使用 癌症 揭示