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SAM Method as an Approach to Select Candidates for Human Prostate Cancer Markers
[chapter]
2005
Lecture Notes in Computer Science
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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
2012
Drug Discovery Today
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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
2009
Drug Discovery Today
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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
2021
International Journal of Molecular Sciences
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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
2005
Genome Biology
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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
2015
BioMed Research International
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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
2011
PLoS ONE
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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
2008
Human Genetics
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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
2011
Advances in Adaptive Data Analysis
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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
2006
Clinical Cancer Research
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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
2016
Cancer Medicine
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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
2017
Journal of Steroid Biochemistry and Molecular Biology
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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
2015
EJIFCC
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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
2017
Scientific Reports
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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
2019
Prostate Cancer and Prostatic Diseases
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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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