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SAM Method as an Approach to Select Candidates for Human Prostate Cancer Markers [chapter]

A C Q Simoes, A M da Silva, S Verjovski-Almeida, E M Reis
2005 Lecture Notes in Computer Science  
In order to select gene markers among differentially expressed transcripts identified from tumoral prostate, we have applied a filter and Significance Analysis of Microarrays (SAM) as the feature selection  ...  SAM was run using either two-class, unpaired data analysis with Gleason 5-6 and Gleason 9-10 samples, or multiclass response analysis with an additional category of Gleason 7-8.  ...  In the present work we have re-analyzed this complete microarray dataset using four different filters and SAM as feature selection method.  ... 
doi:10.1007/11532323_23 fatcat:gni56oi5dfaoncdklpn2lvsxz4

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2012 Drug Discovery Today  
Acknowledgements We wish to thank Dr Pavel Pospisil and Dr Lakshmanan K. Iyer for their helpful discussions in this project.  ...  Finally, seven candidate genes that are highly overproduced were selected as potential diagnostic markers for lung cancer.  ...  candidate genes associated with prostate cancer.  ... 
doi:10.1016/j.drudis.2011.12.006 pmid:22178890 fatcat:c7k3puzntbhcrmzjlw6uvgxhny

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2009 Drug Discovery Today  
Acknowledgements We wish to thank Dr Pavel Pospisil and Dr Lakshmanan K. Iyer for their helpful discussions in this project.  ...  Finally, seven candidate genes that are highly overproduced were selected as potential diagnostic markers for lung cancer.  ...  candidate genes associated with prostate cancer.  ... 
doi:10.1016/j.drudis.2008.12.005 pmid:19135549 fatcat:plsts2psuvclneuhgd5tlianwi

CRISPR Screen Contributes to Novel Target Discovery in Prostate Cancer

Takuya Tsujino, Kazumasa Komura, Teruo Inamoto, Haruhito Azuma
2021 International Journal of Molecular Sciences  
Prostate cancer (PCa) is one of the common malignancies in male adults.  ...  In this review, we focus on how CRISPR screen for PCa performed to date has contributed to the identification of biologically critical and clinically relevant target genes.  ...  Introduction Prostate cancer (PCa) accounts for 1.6 million cases and 366,000 deaths worldwide each year [1] .  ... 
doi:10.3390/ijms222312777 pmid:34884583 pmcid:PMC8658029 fatcat:3e3hxcmp2rbsjjgacj5aan3eo4

A DNA microarray survey of gene expression in normal human tissues

Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack
2005 Genome Biology  
In addition, our analysis identifies potential molecular markers for detection of injury to specific organs and tissues, and provides a foundation for selection of potential targets for selective anticancer  ...  Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states.  ...  This work was sup-ported by a grant from the National Cancer Institute. P.O.B is an investigator of the Howard Hughes Medical Institute.  ... 
doi:10.1186/gb-2005-6-3-r22 pmid:15774023 pmcid:PMC1088941 fatcat:je6z6k5jgbhsjnez46migg3aam

A Meta-Analysis Strategy for Gene Prioritization Using Gene Expression, SNP Genotype, and eQTL Data

Jingmin Che, Miyoung Shin
2015 BioMed Research International  
This method was evaluated on two publicly available datasets regarding prostate cancer and lung cancer to identify disease-related genes.  ...  For this purpose, many earlier approaches attempted to prioritize candidate genes using gene expression profiles or SNP genotype data, but they often suffer from producing many false-positive results.  ...  Chu, "Significance analysis of microarrays applied to the ionizing radiation response, " Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 9, pp. 5116-5121,  ... 
doi:10.1155/2015/576349 pmid:25874220 pmcid:PMC4385654 fatcat:ho3r7rvjyvcwvgqzgtzpimxcqe

Modulation of Androgen Receptor Signaling in Hormonal Therapy-Resistant Prostate Cancer Cell Lines

Rute B. Marques, Natasja F. Dits, Sigrun Erkens-Schulze, Wilfred F. J. van IJcken, Wytske M. van Weerden, Guido Jenster, Laszlo Tora
2011 PLoS ONE  
Finally, the androgen-regulated genes ENDOD1, MCCC2 and ACSL3 were selected as potential disease markers for RT-PCR quantification in a distinct set of human prostate specimens.  ...  Prostate epithelial cells depend on androgens for survival and function.  ...  Further, we would like to acknowledge the pathologists Arno van Leenders and Theo van de Kwast for the histopathological analysis of the patient samples. Author Contributions  ... 
doi:10.1371/journal.pone.0023144 pmid:21829708 pmcid:PMC3150397 fatcat:nl42rncd2zh7ph7bct5ftauctq

A haplotype at chromosome Xq27.2 confers susceptibility to prostate cancer

Brian L. Yaspan, Kate M. McReynolds, J. Bradford Elmore, Joan P. Breyer, Kevin M. Bradley, Jeffrey R. Smith
2008 Human Genetics  
We conducted an association study to identify risk variants for familial prostate cancer within the HPCX locus at Xq27 among Americans of Northern European descent.  ...  The haplotype predisposed to prostate cancer with an odds ratio of 3.41 (95% CI 1.04-11.17, P = 0.034) among test subjects.  ...  Acknowledgments We extend particular thanks to the study participants and to Drs Joseph Smith, Michael Cookson, Sam Chang, Richard Hock, William Maynard, Jason Pereira, and William Dupont.  ... 
doi:10.1007/s00439-008-0486-8 pmid:18350320 pmcid:PMC2811403 fatcat:y6a4s35pwvc6tbyckxhdjyov34

ON GENE SELECTION AND CLASSIFICATION FOR CANCER MICROARRAY DATA USING MULTI-STEP CLUSTERING AND SPARSE REPRESENTATION

LIPING JING, MICHAEL K. NG, TIEYONG ZENG
2011 Advances in Adaptive Data Analysis  
Experimental results on public available microarray data show that the proposed framework often outperforms the existing feature selection and prediction methods such as SAM, information gain (IG), and  ...  In this work, a novel framework (named by SGS) is presented for significant genes selection and efficient cancer case classification.  ...  The number of selected genes is 20 for colon, 49 for leukemia, 33 for breast (LN), 36 for breast (ER), 32 for SRBCT, 43 for prostate cancer cDNA data, and 21 for prostate cancer oligodata.  ... 
doi:10.1142/s1793536911000763 fatcat:uulnskvo7fhy5inkr2xjqshqru

Prognostic DNA Methylation Biomarkers in Ovarian Cancer

S. H. Wei
2006 Clinical Cancer Research  
Experimental Design:We used a microarray approach to identify methylated loci prognostic for reduced progression-free survival (PFS) in advanced ovarian cancer patients.Two data set classification algorithms  ...  Such ovarian cancer biomarkers represent a promising approach for the assessment and management of this devastating disease.  ...  In rare cases, methylation of single loci is prognostic for specific cancer types. For example, methylation of GSTP1 has been shown as a highly specific marker for prostate cancer (2, 3) .  ... 
doi:10.1158/1078-0432.ccr-05-1551 pmid:16675572 fatcat:zexszdxycbgxrhrmgvydrjskxi

Geraniol suppresses prostate cancer growth through down-regulation of E2F8

Sanghoon Lee, Yu Rang Park, Su-Hwa Kim, Eun-Jung Park, Min Ji Kang, Insuk So, Jung Nyeo Chun, Ju-Hong Jeon
2016 Cancer Medicine  
We used an unsupervised feature selection method to determine 5000 genes of high variance across all microarray samples [16] and then performed clValid on the data of 5000 genes to measure an optimized  ...  For supervised classification, Random Forest, which is an ensemble learning method for classification and regression, was used to validate the clusters [20] .  ... 
doi:10.1002/cam4.864 pmid:27683099 pmcid:PMC5083744 fatcat:pbacwujpnvfy3hsttw7dwqljui

The importance of DNA methylation in prostate cancer development

Charles E. Massie, Ian G. Mills, Andy G. Lynch
2017 Journal of Steroid Biochemistry and Molecular Biology  
After briefly reviewing the nature of DNA methylation, its general role in cancer and the tools available to interrogate it, we consider the literature surrounding DNA methylation as relating to prostate  ...  cancer.  ...  One study aiming to identify prognostic methylation markers for prostate cancer highlighted over one hundred candidate genomic loci [49] .  ... 
doi:10.1016/j.jsbmb.2016.04.009 pmid:27117390 fatcat:4qrpsv6yovgqva5kjexp7wflam

Metabolomics and its Application to the Development of Clinical Laboratory Tests for Prostate Cancer

Jonathan E McDunn, Steven M Stirdivant, Lisa A Ford, Robert L Wolfert
2015 EJIFCC  
The outlook is bright for metabolomic technology to address clinical diagnostic needs for prostate cancer patient management.  ...  Metabolomics has shown its utility to complement and augment traditional clinical approaches as well as emerging genomic, transcriptomic and proteomic methodologies, and is expected to play a key role  ...  Instead of consuming SAM for polyamine biosynthesis, the prostate cancer cell that can convert SAM to S-adenosylhomocysteine (by using SAM as a methyl donor) would also produce cysteine.  ... 
pmid:27683485 pmcid:PMC4975355 fatcat:shtmmcmvlvbrrno2xeqbsuuiqe

A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness

John Lai, Leire Moya, Jiyuan An, Andrea Hoffman, Srilakshmi Srinivasan, Janaththani Panchadsaram, Carina Walpole, Joanna L. Perry-Keene, Suzanne Chambers, Melanie L. Lehman, Colleen C. Nelson, Judith A. Clements (+1 others)
2017 Scientific Reports  
We propose that TG-PCA3 STR has both diagnostic and prognostic potential for prostate cancer.  ...  There is a growing interest in STRs as modulators of disease 12 , with recent concerted efforts being made in characterizing STRs in the human genome using high-throughput DNA sequencing approaches 3,13  ...  Acknowledgements We thank study participants who kindly donated tissue to the Australian Prostate Cancer BioResource (APCB).  ... 
doi:10.1038/s41598-017-16700-y pmid:29203868 pmcid:PMC5715103 fatcat:rzpeyukykzg7rhlr3kusfqxeii

Approaches to urinary detection of prostate cancer

Jillian N. Eskra, Daniel Rabizadeh, Christian P. Pavlovich, William J. Catalona, Jun Luo
2019 Prostate Cancer and Prostatic Diseases  
In this review, we focus on important advances as well as future efforts needed to drive clinical innovation in this area of urine biomarker research for prostate cancer detection and prognostication.  ...  Prostate cancer is the most common cancer in American men that ranges from low risk states amenable to active surveillance to high-risk states that can be lethal especially if untreated.  ...  Acknowledgements The authors acknowledge funding support from the Prostate Cancer Foundation, Urological Research Foundation, and NIH grants U54CA199091, P50CA180995, and X01HG009642 to WJC.  ... 
doi:10.1038/s41391-019-0127-4 pmid:30655600 pmcid:PMC6640078 fatcat:a75ow2vedzhvpo4yfhobsbjesa
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