A new analysis approach of epidermal growth factor receptor pathway activation patterns provides insights into cetuximab resistance mechanisms in head and neck cancer

The pathways downstream of the epidermal growth factor receptor (EGFR) have often been implicated to play crucial roles in the development and progression of various cancer types. Different authors have proposed models in cell lines in which they study the modes of pathway activities after perturbation experiments. It is prudent to believe that a better understanding of these pathway activation patterns might lead to novel treatment concepts for cancer patients or at least allow a better stratification of patient collectives into different risk groups or into groups that might respond to different treatments. Traditionally, such analyses focused on the individual players of the pathways. More recently in the field of systems biology, a plethora of approaches that take a more holistic view on the signaling pathways and their downstream transcriptional targets has been developed. Fertig et al. have recently developed a new method to identify patterns and biological process activity from transcriptomics data, and they demonstrate the utility of this methodology to analyze gene expression activity downstream of the EGFR in head and neck squamous cell carcinoma to study cetuximab resistance. Please see related article: http://www.biomedcentral.com/1471-2164/13/16

DNA Microarray Data Analysis: A New Survey on Biclustering

There are subsets of genes that have similar behavior under subsets of conditions, so we say that they coexpress, but behave independently under other subsets of conditions. Discovering such coexpressions can be helpful to uncover genomic knowledge such as gene networks or gene interactions. That is why, it is of utmost importance to make a simultaneous clustering of genes and conditions to identify clusters of genes that are coexpressed under clusters of conditions. This type of clustering is called biclustering.Biclustering is an NP-hard problem. Consequently, heuristic algorithms are typically used to approximate this problem by finding suboptimal solutions. In this paper, we make a new survey on biclustering of gene expression data, also called microarray data

Knowledge-constrained projection of high-dimensional data

Projection of high-dimensional data is usually done by reducing dimensionality of the data and transforming the data to the latent space. We created synthetic data to simulate real gene-expression datasets and we tested methods on both synthetic and real data. With this work we address the visualization of our data through implementation of regularized singular value decomposition (SVD) for biclustering using L0-norm and L1-norm. Additional knowledge is introduced to the model through regularization with the two prior adjacency matrices. We show that L0-norm SVD and L1-norm SVD give better results than standard SVD

双向聚类方法综述

传统的聚类方法由于无法提取样本和变量间的局部对应关系,并且当数据具有高维性和稀疏性时表现不佳,因此学者们提出了双向聚类,基于样本和变量间的局部关系,同时对样本和变量进行聚类,形成一个子矩阵的聚类结果。近年来,双向聚类发展迅速,在基因分析、文本聚类、推荐系统等领域应用广泛。首先,对双向聚类方法进行梳理与归纳,重点阐述稀疏双向聚类、谱双向聚类和信息双向聚类三类方法,分析它们之间的区别和联系,并且介绍这三类方法在多源数据的整合分析、多层聚类、半监督学习以及集成学习上的发展现状和趋势;其次,重点介绍双向聚类在基因分析、文本聚类、推荐系统等领域的应用研究情况;最后,结合大数据时代的数据特征和双向聚类的存在的问题,展望双向聚类未来的研究方向