A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies.

نویسندگان

  • Larsson Omberg
  • Gene H Golub
  • Orly Alter
چکیده

We describe the use of a higher-order singular value decomposition (HOSVD) in transforming a data tensor of genes x "x-settings," that is, different settings of the experimental variable x x "y-settings," which tabulates DNA microarray data from different studies, to a "core tensor" of "eigenarrays" x "x-eigengenes" x "y-eigengenes." Reformulating this multilinear HOSVD such that it decomposes the data tensor into a linear superposition of all outer products of an eigenarray, an x- and a y-eigengene, that is, rank-1 "subtensors," we define the significance of each subtensor in terms of the fraction of the overall information in the data tensor that it captures. We illustrate this HOSVD with an integration of genome-scale mRNA expression data from three yeast cell cycle time courses, two of which are under exposure to either hydrogen peroxide or menadione. We find that significant subtensors represent independent biological programs or experimental phenomena. The picture that emerges suggests that the conserved genes YKU70, MRE11, AIF1, and ZWF1, and the processes of retrotransposition, apoptosis, and the oxidative pentose phosphate pathway that these genes are involved in, may play significant, yet previously unrecognized, roles in the differential effects of hydrogen peroxide and menadione on cell cycle progression. A genome-scale correlation between DNA replication initiation and RNA transcription, which is equivalent to a recently discovered correlation and might be due to a previously unknown mechanism of regulation, is independently uncovered.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Principal Component Analysis using Singular Value Decomposition of Microarray Data

A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented...

متن کامل

Modified Laplace Decomposition Method for Singular IVPs in the second-Order Ordinary Differential Equations

  In this paper, we use modified Laplace decomposition method to solving initial value problems (IVP) of the second order ordinary differential equations. Theproposed method can be applied to linear and nonlinearproblems    

متن کامل

Multiscale Analysis for Higher-order Tensors

The widespread use of multisensor technology and the emergence of big datasets have created the need to develop tools to reduce, approximate, and classify large and multimodal data such as higher-order tensors. While early approaches focused on matrix and vector based methods to represent these higher-order data, more recently it has been shown that tensor decomposition methods are better equip...

متن کامل

On the interconnection between the higher-order singular values of real tensors

A higher-order tensor allows several possible matricizations (reshapes into matrices). The simultaneous decay of singular values of such matricizations has crucial implications on the low-rank approximability of the tensor via higher-order singular value decomposition. It is therefore an interesting question which simultaneous properties the singular values of different tensor matricizations ac...

متن کامل

Noise Effects on Modal Parameters Extraction of Horizontal Tailplane by Singular Value Decomposition Method Based on Output Only Modal Analysis

According to the great importance of safety in aerospace industries, identification of dynamic parameters of related equipment by experimental tests in operating conditions has been in focus. Due to the existence of noise sources in these conditions the probability of fault occurrence may increases. This study investigates the effects of noise in the process of modal parameters identification b...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Proceedings of the National Academy of Sciences of the United States of America

دوره 104 47  شماره 

صفحات  -

تاریخ انتشار 2007