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Predicting Cellular Growth from Gene Expression Signatures

Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya, Andrey Rzhetsky
2009 PLoS Computational Biology  
We find that the expression levels of a small set of genes accurately predict the instantaneous growth rate of any cellular culture, robust to changing biological conditions, experimental methods, and  ...  We investigate the biological significance of the identified gene expression signature from multiple perspectives: by perturbing the regulatory network through the Ras/PKA pathway, observing strong up-regulation  ...  Model-Based Prediction of Instantaneous Growth Rates from Expression Data The set of growth-specific calibration genes defined above represents a quantitative signature of a cellular culture's transcriptional  ... 
doi:10.1371/journal.pcbi.1000257 pmid:19119411 pmcid:PMC2599889 fatcat:bi6l2cosmfbqxk2k57zq3akhya

Anchorage-independent cell growth signature identifies tumors with metastatic potential

S Mori, J T Chang, E R Andrechek, N Matsumura, T Baba, G Yao, J W Kim, M Gatza, S Murphy, J R Nevins
2009 Oncogene  
Here we describe the development of a signature of anchorage-independent growth, show that the signature exhibits characteristics of deregulated mitochondrial function and then demonstrate that the signature  ...  The oncogenic phenotype is complex, resulting from the accumulation of multiple somatic mutations that lead to the deregulation of growth regulatory and cell fate controlling activities and pathways.  ...  This work was supported by a grant (5U54CA-112952-05) from the NIH/NCI to JRN. SM was a research fellow of the Uehara Memorial Foundation and is a visiting scholar of Riken Genome Science Center.  ... 
doi:10.1038/onc.2009.139 pmid:19483725 pmcid:PMC3008357 fatcat:etuyiqv57jeofpkqkkchhpcfdu

Bromodomain 4 activation predicts breast cancer survival

N. P. S. Crawford, J. Alsarraj, L. Lukes, R. C. Walker, J. S. Officewala, H. H. Yang, M. P. Lee, K. Ozato, K. W. Hunter
2008 Proceedings of the National Academy of Sciences of the United States of America  
Further in vitro analysis shows that Brd4 modulates extracellular matrix gene expression, a class of genes frequently present in metastasis-predictive gene signatures.  ...  expression signature that predicts outcome in multiple breast cancer datasets.  ...  of many genes that are frequently observed as components of metastasis-predictive gene expression signatures.  ... 
doi:10.1073/pnas.0710331105 pmid:18427120 pmcid:PMC2359777 fatcat:rvy3ti4twzappn62he6jyv6ih4

A Genome-Wide Systematic Analysis Reveals Different and Predictive Proliferation Expression Signatures of Cancerous vs. Non-Cancerous Cells

Yedael Y. Waldman, Tamar Geiger, Eytan Ruppin, Marshall S. Horwitz
2013 PLoS Genetics  
Furthermore, combining cancerous and non-cancerous proliferation signatures leads to enhanced prediction of patient outcome and gene essentiality in cancer.  ...  Here we employ a complementary approach and assign each gene a cancer Proliferation Index (cPI) that quantifies the association between its expression levels and growth rate measurements across 60 cancer  ...  predict survival outcome analyzing clinical samples Gene expression signatures can classify tumor classes and predict patient survival [33] [34] [35] .  ... 
doi:10.1371/journal.pgen.1003806 pmid:24068970 pmcid:PMC3778010 fatcat:dykdgkyeunbync3dii2feeoooq

Integration of biological knowledge and gene expression data for biomarker selection

Sally A. Amundson, Lubomir B. Smilenov
2010 Cancer Biology & Therapy  
From the early days of gene expression microarray analysis, many studies have focused on the development of signatures predictive of long-term survival or the response to specific therapies.  ...  to identify multiple predictive signatures from the same data set that performed equally well.  ... 
doi:10.4161/cbt.10.12.13731 pmid:20948301 pmcid:PMC3230290 fatcat:xdnhaywwnvhfnm5qtd4tkmrn4y

Identification and prioritization of candidate genes for symptom variability in breast cancer survivors based on disease characteristics at the cellular level

Theresa Koleck, Yvette Conley
2016 Breast Cancer : Targets and Therapy  
A list of genes evaluated within five multigene expression profiles for breast cancer was compiled.  ...  Initial candidate gene identification was based on genes evaluated as part of multigene expression profiles for breast cancer, which are commonly used in the clinical setting to characterize the biology  ...  Lists of genes were obtained from the following locations in March 2014: the eleven-gene expression profile (Jerevall et al), 28 the 14-gene prognostic expression signature (Tutt et al), 23 the 21-gene  ... 
doi:10.2147/bctt.s88434 pmid:27022301 pmcid:PMC4790538 fatcat:6jo6ans4vnbr5ai3qam3sizq3y

Immunoautophagy-Related Long Noncoding RNA (IAR-lncRNA) Signature Predicts Survival in Hepatocellular Carcinoma

Yulu Wang, Fangfang Ge, Amit Sharma, Oliver Rudan, Maria F. Setiawan, Maria A. Gonzalez-Carmona, Miroslaw T. Kornek, Christian P. Strassburg, Matthias Schmid, Ingo G. H. Schmidt-Wolf
2021 Biology  
This has led to the possibility of developing a prognostic signature based on immuno-autophagy-related (IAR) genes.  ...  The obtained signature predicted the high-risk HCC group with shorter overall survival, and was further associated with clinical characteristics such as tumor grade (t = 10.918, p = 0.001).  ...  In the context of autophagy-related genes (ATG), lower expression was previously observed in HCC, which was predicted to contribute to tumor growth and the poor prognosis of the disease [13, 14] .  ... 
doi:10.3390/biology10121301 pmid:34943216 pmcid:PMC8698564 fatcat:y3tq7l4isbfyxf6s5fm4yycq7i

Can Systems Biology Understand Pathway Activation? Gene Expression Signatures as Surrogate Markers for Understanding the Complexity of Pathway Activation

Hiraku Itadani, Shinji Mizuarai, Hidehito Kotani
2008 Current Genomics  
However, the biological implication of those gene expression signatures is often unclear.  ...  cases, prediction of clinical outcomes.  ...  STATISTICAL PREDICTION OF PATHWAY ACTIV-ITY BY SIGNTAURE GENE EXPRESSION Practical issues in pathway signatures include how to select genes from tens of thousands of genes on a microarray and how to predict  ... 
doi:10.2174/138920208785133235 pmid:19517027 pmcid:PMC2694555 fatcat:bgy3ddmd4bh2tguw34gkh622iu

Gene signatures of drug resistance predict patient survival in colorectal cancer

Y Zheng, J Zhou, Y Tong
2014 The Pharmacogenomics Journal  
On the basis of the three gene signatures, three score systems were developed to stratify patients from sensitive to resistance.  ...  Using survival prediction analysis, we have identified three independent gene signatures, which are associated with sensitivity of colorectal cancer cells to 5-FU, oxaliplatin or irinotecan.  ...  type and different clinical behavior. 44 Gene expression profiling of peritoneal metastases from appendiceal and colon cancer demonstrates unique biologic signatures and predicts patient outcomes.  ... 
doi:10.1038/tpj.2014.45 pmid:25179828 pmcid:PMC4381104 fatcat:664yez3u7bdgjagji55e4ppwai

An integrative analysis of cancer gene expression studies using Bayesian latent factor modeling

Daniel Merl, Julia Ling-Yu Chen, Jen-Tsan Chi, Mike West
2009 Annals of Applied Statistics  
expression.  ...  The statistical methodologies employed here draw heavily on Bayesian sparse factor models for identifying, modularizing and correlating with clinical outcome these signatures of aggregate changes in gene  ...  Any opinions, findings and conclusions or recommendations expressed in this work are those of the authors and do not necessarily reflect the views of the NSF or NIH.  ... 
doi:10.1214/09-aoas261 pmid:20953268 pmcid:PMC2954437 fatcat:rar5i76mnbd7ll56mvrphhcady

Identification of a Cyclin D1 Network in Prostate Cancer That Antagonizes Epithelial–Mesenchymal Restraint

Xiaoming Ju, Mathew C. Casimiro, Michael Gormley, Hui Meng, Xuanmao Jiao, Sanjay Katiyar, Marco Crosariol, Ke Chen, Min Wang, Andrew A. Quong, Michael P. Lisanti, Adam Ertel (+1 others)
2013 Cancer Research  
Gene signatures have provided improved prognostic indicators of human prostate cancer.  ...  Endogenous cyclin D1 enhanced Wnt and ES cell gene expression and expanded a prostate stem cell population.  ...  D1 expression signature in comparison to a 4-gene signature from 2.6 to 3.75 (P < 0.002).  ... 
doi:10.1158/0008-5472.can-13-1313 pmid:24282282 pmcid:PMC3914674 fatcat:oeuzz3qntjewjnuazqya74qrta

The Origins of Breast Cancer Prognostic Gene Expression Profiles

L. Lukes, N. P.S. Crawford, R. Walker, K. W. Hunter
2009 Cancer Research  
Recent high profile clinical trials show that microarray-based gene expression profiling has the potential to become an important tool for predicting prognosis in breast cancer.  ...  To investigate if these gene expression signatures were of somatic or germline origin and to assess the contribution of different cell types to the induction of these signatures, we have performed a series  ...  The cellular origins of the inherited components of the predictive gene signatures were further investigated using a transplant strategy.  ... 
doi:10.1158/0008-5472.can-08-3520 pmid:19118016 pmcid:PMC2613551 fatcat:2betcz2og5fofeua4ch2w4cxxm

Can Stroma Reaction Predict Cancer Lethality?

M. R. Freeman, Q. Li, L. W. K. Chung
2013 Clinical Cancer Research  
West pioneered an approach that involves characterizing gene expression patterns of two relatively pure populations of stromal cells isolated from soft-tissue tumors, the desmoid-type fibromatosis (DTF  ...  or cellular blood-based biomarkers.  ...  Authors' Contributions Can Stroma Reaction Predict Cancer Lethality? Updated version 10 To request permission to re-use all or part of this article, contact the AACR Publications Department at  ... 
doi:10.1158/1078-0432.ccr-13-1694 pmid:24009149 pmcid:PMC3983789 fatcat:4t66iszjwnabji3bfec7cyepku

Developing gene expression signatures of pathway deregulation in tumors

J. W. Watters, C. J. Roberts
2006 Molecular Cancer Therapeutics  
This review discusses recent advances in the identification of gene expression -based signatures of pathway deregulation and how this information may lead to improved therapeutic response prediction.  ...  Therefore, developing gene expression signatures of pathway activation status using model systems or human tumor samples may enable a more reliable measurement of pathway activity.  ...  This signaling cascade affects multiple cellular processes and results in a gene expression ''signature'' of pathway activity.  ... 
doi:10.1158/1535-7163.mct-06-0340 pmid:17041087 fatcat:377chrisqbdwtppbrkdwtd2ymi

Prediction of Drug Efficacy in Colon Cancer Preclinical Models Using a Novel Ranking Method of Gene Expression

Justine Fritz, Olivier Lefebvre, Aurore Fernandez, Jordane Schmidt, Dominique Bagnard
2020 Cancers  
The presence of stromal cells in tumors is altering the significance of molecular profiling when using standard methods of gene expression quantification.  ...  The score for each target gene obtained after normalization, is aimed to be predictive of targeted therapies efficiency.  ...  Laurent Jacob for helpful discussion on the normalization process and Oncodesign for providing access to their cohort of PDX models and performing the in vivo evaluation of the drugs to validate the predictive  ... 
doi:10.3390/cancers12010149 pmid:31936310 fatcat:swg767gvhvfy5nzyue2w3pg63e
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