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Computational purification of tumor gene expression data

Amit Deshwar, Gerald Quon, Quaid Morris
2011 BMC Bioinformatics  
We are currently generating a compendium of purified gene expression profiles from 1600 tumor samples representing 15 different types of solid cancer using archival data from GEO.  ...  Materials and methods We have developed ISOpure [4] , a computational method to purify tumor gene expression profiles using reference samples of healthy tissue to model the contribution of healthy tissue  ... 
doi:10.1186/1471-2105-12-s11-a9 pmcid:PMC3277247 fatcat:eazq5t6npzeh5elh3bapxax3t4

Purity for clarity: the need for purification of tumor cells in DNA microarray studies

D de Ridder, C E van der Linden, T Schonewille, W A Dik, M J T Reinders, J J M van Dongen, F J T Staal
2005 Leukemia  
A tumor load of at least 90% leads to identification of at most 5% false-positive genes.  ...  The simulations demonstrated that a tumor load of less than 75% can lead to up to 25% erroneously identified genes.  ...  (b) Comparison of gene expression profile of purified and nonpurified T-ALL samples of the same patient, for T-ALL1, 89% tumor load before purification and T-ALL2, 62% tumor load before purification.  ... 
doi:10.1038/sj.leu.2403685 pmid:15744349 fatcat:bjfd2yjbmzah7nazmb3l6yg6bq

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

Gerald Quon, Syed Haider, Amit G Deshwar, Ang Cui, Paul C Boutros, Quaid Morris
2013 Genome Medicine  
We describe a computational purification tool, ISOpure, which directly addresses the effects of variable contamination by normal tissue in clinical tumor specimens.  ...  ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample, and an estimate of the proportion of RNA originating  ...  This study was conducted with the support of the Ontario Institute for Cancer Research to PCB through funding provided by the Government of Ontario.  ... 
doi:10.1186/gm433 pmid:23537167 pmcid:PMC3706990 fatcat:jftzohfwezgf5ekz37ymnfnpqy

DNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers

F J T Staal, M van der Burg, L F A Wessels, B H Barendregt, M R M Baert, C M M van den Burg, C Van Huffel, A W Langerak, V H J van der Velden, M J T Reinders, J J M van Dongen
2003 Leukemia  
Microarrays for gene expression profiling are rapidly becoming important research tools for the identification of novel markers, for example, for novel classification of leukemias and lymphomas.  ...  The gene expression profiles were evaluated with Affymetrix U95A chips containing 12 600 human genes.  ...  Acknowledgements We thank members of the Molecular Immunology unit from the Department of Immunology for stimulating discussions.  ... 
doi:10.1038/sj.leu.2402974 pmid:12835720 fatcat:tdg23iiqjfczdjuqgpcl4q4fpu

Determining cell type abundance and expression from bulk tissues with digital cytometry

Aaron M. Newman, Chloé B. Steen, Chih Long Liu, Andrew J. Gentles, Aadel A. Chaudhuri, Florian Scherer, Michael S. Khodadoust, Mohammad S. Esfahani, Bogdan A. Luca, David Steiner, Maximilian Diehn, Ash A. Alizadeh
2019 Nature Biotechnology  
We now introduce CIBERSORTx, a machine learning method that extends this framework to infer cell-type-specific gene expression profiles without physical cell isolation.  ...  By minimizing platform-specific variation, CIBERSORTx also allows the use of single-cell RNA-sequencing data for large-scale tissue dissection.  ...  Right: Analysis of the impact of sample size on group-mode gene expression purification for three FL tumor cell subsets, as assessed by Spearman correlation against corresponding FACSpurified GEPs ("ground  ... 
doi:10.1038/s41587-019-0114-2 pmid:31061481 pmcid:PMC6610714 fatcat:rqlmil5vlnas3jxahw7ivwjitm

Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks

F J T Staal, G Cario, G Cazzaniga, T Haferlach, M Heuser, W-K Hofmann, K Mills, M Schrappe, M Stanulla, L U Wingen, J J M van Dongen, B Schlegelberger
2006 Leukemia  
The activities of the Genomics/Proteomics project of the German Competence Network 'Acute and Chronic Leukemias' have been supported by BMBF Grant 01GI0378.  ...  Acknowledgements The excellent technical assistance of Marcel Tauscher in performing the multi-center quality rounds is gratefully acknowledged.  ...  What is the minimum tumor load to make meaningful statements about the expression of certain genes in the cells of interest? What is RNA of sufficient quality?  ... 
doi:10.1038/sj.leu.2404274 pmid:16761018 fatcat:4mv5be43nndjhiihbu4dwmvgfy

Cancer antigen discovery is enabled by RNA-sequencing of highly purified malignant and non-malignant cells

Martin J Scurr, Alexander Greenshields-Watson, Emma Campbell, Michelle Somerville, Yuan Chen, Sarah L Hulin-Curtis, Stephanie E A Burnell, James A Davies, Michael M Davies, Rachel Hargest, Simon Phillips, Adam D Christian (+6 others)
2020 Clinical Cancer Research  
; tumor cell purification was essential to reveal these genes.  ...  It is expressed in many tumors and is strongly immunogenic in patients with cancers originating from a variety of sites.  ...  C, Comparison of expression levels between tumor and solid tissue normal in available TCGA data, scaled by gene.  ... 
doi:10.1158/1078-0432.ccr-19-3087 pmid:32122920 fatcat:imno6m3m6bdc7lizcbaoazprem

A Circulating Tumor Cell-RNA Assay for Assessment of Androgen Receptor Signaling Inhibitor Sensitivity in Metastatic Castration-Resistant Prostate Cancer

Yu Jen Jan, Junhee Yoon, Jie-Fu Chen, Pai-Chi Teng, Nu Yao, Shirley Cheng, Amber Lozano, Gina C.Y. Chu, Howard Chung, Yi-Tsung Lu, Pin-Jung Chen, Jasmine J. Wang (+12 others)
2019 Theranostics  
We also showed that the genes in CTC-PCS1 panel are highly expressed in PCa cell lines and lowly expressed in background WBCs.  ...  The PCS1 Z scores of each sample were computed and compared with ARSI treatment sensitivity.  ...  For the visualization of the gene expression data, hierarchical clustering of the CTC gene expression profiles was done with two distance measures: Euclidean distance for gene clustering and cosine distance  ... 
doi:10.7150/thno.34485 pmid:31244925 pmcid:PMC6568173 fatcat:pvmc4qco25czriqek22mcffiri

Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway

Zainab Jagani, E Lorena Mora-Blanco, Courtney G Sansam, Elizabeth S McKenna, Boris Wilson, Dongshu Chen, Justin Klekota, Pablo Tamayo, Phuong T L Nguyen, Michael Tolstorukov, Peter J Park, Yoon-Jae Cho (+13 others)
2010 Nature Medicine  
Consistent with this, we show the presence of a Hh-Gli-activated gene expression profile in primary MRTs and show that GLI1 drives the growth of SNF5-deficient MRT cells in vitro and in vivo.  ...  We show that Snf5 localizes to Gli1-regulated promoters and that loss of Snf5 leads to activation of the Hh-Gli pathway. Conversely, re-expression of SNF5 in MRT cells represses GLI1.  ...  of gene expression 21, 22 .  ... 
doi:10.1038/nm.2251 pmid:21076395 pmcid:PMC3859448 fatcat:rcbrh7o4indznggpc5iccs27vu

RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples

C. E. Rogler
2004 Nucleic Acids Research  
In REMs with real samples, we detected organ-specific expression of albumin, Hnf-4 and Igfbp-1, in a set of mouse organ cDNA populations and c-Myc expression in tumor samples in paired tumor/normal tissue  ...  We used simultaneous hybridization with test and reference (housekeeping) genes to calculate an expression ratio based on normalization with the endogenous reference gene.  ...  ACKNOWLEDGEMENTS The authors thank Dr Liang Zhu and Dr David Shafritz for critical reading of this manuscript.  ... 
doi:10.1093/nar/gnh116 pmid:15329382 pmcid:PMC516075 fatcat:f5aiozi5bngtfgbkkom543lk4u

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

Assaf Magen, Jia Nie, Thomas Ciucci, Samira Tamoutounour, Yongmei Zhao, Monika Mehta, Bao Tran, Dorian B. McGavern, Sridhar Hannenhalli, Rémy Bosselut
2019 Cell Reports  
Computational approaches to characterize subpopulations identify TIL transcriptomic patterns strikingly distinct from acute and chronic anti-viral responses and dominated by diversity among T-bet-expressing  ...  Here, we use single-cell mRNA sequencing to analyze the response of tumor-specific CD4+ TILs and draining lymph node (dLN) T cells.  ...  This work used the NIH high-performance computing cluster and was supported by the Intramural Research Program of the National Cancer Institute, Center for Cancer Research, NIH.  ... 
doi:10.1016/j.celrep.2019.10.131 pmid:31801070 pmcid:PMC6934378 fatcat:7ndhxdhcubehlcu7clrazztwam

Tumor Derived SIGLEC Family Genes May Play Roles in Tumor Genesis, Progression, and Immune Microenvironment Regulation

Zheng Chen, Mincheng Yu, Lei Guo, Bo Zhang, Shuang Liu, Wentao Zhang, Binghai Zhou, Jiuliang Yan, Qianni Ma, Zhangfu Yang, Yongsheng Xiao, Yongfeng Xu (+2 others)
2020 Frontiers in Oncology  
Our computational analysis showed SIGLEC family genes expressed by tumor cells were associated with tumor behaviors, and they may also influence TME through chemokine axis, playing vital roles in patients  ...  SIGLEC family genes can also be expressed on tumor cells in different cancer types, and though it has been found that SIGLEC genes expressed by immune cells can be exploited by tumors to escape immune  ...  CONCLUSION Our computational analysis showed SIGLEC family genes expressed by tumor cells in different cancer types were related to tumor formation and patients' survival, and they could regulate tumor  ... 
doi:10.3389/fonc.2020.586820 pmid:33240817 pmcid:PMC7681003 fatcat:ajheqbxc5nhvnbrnvgoi5wsiyy

Systems analysis of the prostate tumor suppressor NKX3.1 supports roles in DNA repair and luminal cell differentiation

Chih-Cheng Yang, Alicia Chung, Chia-Yu Ku, Laurence M. Brill, Roy Williams, Dieter A. Wolf
2014 F1000Research  
No Comments Yet 2 1 RESEARCH ARTICLE Systems analysis of the prostate tumor suppressor NKX3.1 supports roles in DNA repair and luminal cell differentiation [v1; ref status: indexed, Abstract NKX3.  ...  Taken together, these data shed new light onto the elusive tumor suppressor activity of NKX3.1, directly implicating this homeoprotein in DNA repair and in driving a gene expression signature indicative  ...  of this tumor suppressor.  ... 
doi:10.12688/f1000research.3818.1 pmid:25177484 pmcid:PMC4141641 fatcat:caams2bprbbmvdh5ibwvne7nee

Inference of immune cell composition on the expression profiles of mouse tissue

Ziyi Chen, Anfei Huang, Jiya Sun, Taijiao Jiang, F. Xiao-Feng Qin, Aiping Wu
2017 Scientific Reports  
Here we report the development of a computational algorithm, ImmuCC, to infer the relative compositions of 25 immune cell types in mouse tissues using microarray-based mRNA expression data.  ...  mouse lymphoid tissues and three different types of tumor tissues.  ...  Recently, a few computational methods have been developed for both human blood and tumor samples based on microarray and RNA-seq expression data [14] [15] [16] [17] .  ... 
doi:10.1038/srep40508 pmid:28084418 pmcid:PMC5233994 fatcat:wlko4pr5zfezna3f3sswoorjn4

Functional variomics and network perturbation: connecting genotype to phenotype in cancer

Song Yi, Shengda Lin, Yongsheng Li, Wei Zhao, Gordon B. Mills, Nidhi Sahni
2017 Nature reviews genetics  
We highlight recent advances in computational and experimental strategies to study the diverse functional and phenotypic consequences of mutations at the base-pair resolution.  ...  A systems-level understanding of how cancer mutations affect signaling networks is pivotal for interpreting the complex genotype-to-phenotype relationships in terms of tumor behavior and patient outcomes  ...  Acknowledgements N.S. would like to acknowledge the following grants: the Cancer Prevention and Research Institute of Texas (CPRIT) New Investigator Grant RR160021, the University of Texas System Rising  ... 
doi:10.1038/nrg.2017.8 pmid:28344341 pmcid:PMC6020840 fatcat:uu5azwnjfvdo5jajywg7u3yhtu
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