Identification of a gene expression signature common to distinct cancer pathways.
TLDR
This method allows retrieval of significant new information and testable hypotheses from a pool of deposited cancer gene expression experiments that are otherwise not apparent or appear insignificant from single measurements.Abstract:
Mutations in cancer-causing genes induce changes in gene expression programs critical for malignant cell transformation. Publicly available gene expression profiles produced by modulating the expression of distinct cancer genes may therefore represent a rich resource for the identification of gene signatures common to seemingly unrelated cancer genes. We combined automatic retrieval with manual validation to obtain a data set of high-quality gene microarray profiles. This data set was used to create logical models of the signaling events underlying the observed expression changes produced by various cancer genes and allowed to uncover unknown and verifiable interactions. Data clustering revealed novel sets of gene expression profiles commonly regulated by distinct cancer genes. Our method allows retrieval of significant new information and testable hypotheses from a pool of deposited cancer gene expression experiments that are otherwise not apparent or appear insignificant from single measurements. The complete results are available through a web-application at http://biodata.ethz.ch/cgi-bin/geologic.read more
Citations
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Journal ArticleDOI
Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm
TL;DR: A new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN) is proposed, mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques.
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Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm
TL;DR: The results obtained show that the proposed methodology is capable of increasing the inference of correct regulations and decreasing false regulations to a high degree and the proposed method sacrifices computational time complexity in both cases due to the hybrid optimization process.
Book ChapterDOI
6.01 – Artificial Neural Networks
Z.R. Yang,Z. Yang +1 more
TL;DR: In this article, the authors focus on two ANN algorithms, namely, multilayer perceptron and self-organizing map, which are used for supervised learning and the latter unsupervised learning.
Journal ArticleDOI
Cancer-related genes in the transcription signature of facioscapulohumeral dystrophy myoblasts and myotubes.
Petr Dmitriev,Petr Dmitriev,Ulykbek Kairov,Thomas Robert,Ana Barat,Vladimir Lazar,Gilles Carnac,Dalila Laoudj-Chenivesse,Yegor S. Vassetzky +8 more
TL;DR: This is the first study demonstrating a similarity between FSHD and cancer cell expression profiles, a finding that might indicate the existence of a common step in the pathogenesis of these two diseases.
Proceedings ArticleDOI
Identification of Genetic Pathway for Cervical Cancer Development Using Rough and Bayesian Theory
TL;DR: Rough Set Theory and Bayesian Network based techniques have been applied and it is possible to find out the distinct cellular pathway for development of cancer from the departure of directed edges of the two networks.
References
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Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Journal ArticleDOI
ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform
Daniel R. Rhodes,Jianjun Yu,K. Shanker,Nandan P. Deshpande,Radhika Varambally,Debashis Ghosh,Terrence R. Barrette,Akhilesh Pandey,Arul M. Chinnaiyan +8 more
TL;DR: ONCOMINE is presented, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses and novel biomarkers and therapeutic targets are discovered.
Journal ArticleDOI
A census of human cancer genes
P. Andrew Futreal,Lachlan J. M. Coin,Mhairi Marshall,Thomas A. Down,Tim Hubbard,Richard Wooster,Nazneen Rahman,Michael R. Stratton +7 more
TL;DR: A 'census' of cancer genes is conducted that indicates that mutations in more than 1% of genes contribute to human cancer.