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Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes

Birte Hellwig, Jan G Hengstler, Marcus Schmidt, Mathias C Gehrmann, Wiebke Schormann, Jorg Rahnenfuhrer
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Further, we present the first comprehensive genome-wide evaluation of the prognostic relevance of bimodal genes.  ...  For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and low expression groups is easier compared to genes with unimodal  ...  Acknowledgements This project was funded by the BMBF (JGH, NGFN project oncoprofile, no.: 01GR0816). Author Details  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-276">doi:10.1186/1471-2105-11-276</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20500820">pmid:20500820</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2892466/">pmcid:PMC2892466</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vd6whimkwjayvmydrxi6gzen2i">fatcat:vd6whimkwjayvmydrxi6gzen2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830104820/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-276?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/ab/78ab797ac69df782c02c2ae3cc0f714cbc925296.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-276"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892466" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A comparison of Methods for Data-Driven Cancer Outlier Discovery, and An Application Scheme to Semisupervised Predictive Biomarker Discovery

Seppo Karrila, Julian Hock Ean Lee, Greg Tucker-Kellogg
<span title="">2011</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
Removing genes with Gaussian distribution is computationally efficient and matches MOST particularly well, while also COPA and OS pick prognostically relevant genes in their top ranks.  ...  Outlier detection is a key enabling technology of the workflow, and aids in identifying the focus genes.  ...  Acknowledgements The authors gratefully acknowledge the support of their employer, Lilly Singapore Centre for Drug Discovery, a wholly owned subsidiary of Eli Lilly and Company.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s6868">doi:10.4137/cin.s6868</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21584264">pmid:21584264</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3091411/">pmcid:PMC3091411</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/turx53fyf5g2jk66cv6mcebp2y">fatcat:turx53fyf5g2jk66cv6mcebp2y</a> </span>
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Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

Pratyaksha Wirapati, Christos Sotiriou, Susanne Kunkel, Pierre Farmer, Sylvain Pradervand, Benjamin Haibe-Kains, Christine Desmedt, Michail Ignatiadis, Thierry Sengstag, Frédéric Schütz, Darlene R Goldstein, Martine Piccart (+1 others)
<span title="2008-07-28">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jbglhnqkwfee7n3dmmcag7huuu" style="color: black;">Breast Cancer Research</a> </i> &nbsp;
Method To address the above issues and to further validate these initial findings, we performed the largest meta-analysis of publicly available breast cancer gene expression and clinical data, which are  ...  Although a previous study demonstrated a prognostic concordance among gene expression signatures, it was limited to only one dataset and did not fully elucidate how the different genes were related to  ...  We dedicate this work to Hans-Martin Schultze, who started the preliminary analysis but succumbed prematurely to metastasis of melanoma.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/bcr2124">doi:10.1186/bcr2124</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18662380">pmid:18662380</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2575538/">pmcid:PMC2575538</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qi2p3xqk5fcfrascv3cf3rm6u4">fatcat:qi2p3xqk5fcfrascv3cf3rm6u4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720012841/https://breast-cancer-research.biomedcentral.com/track/pdf/10.1186/bcr2124?site=breast-cancer-research.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/50/21/50215833f6580314484bf434bc2c304af9dfae92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/bcr2124"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575538" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Overall survival prediction of non-small cell lung cancer by integrating microarray and clinical data with deep learning

Yu-Heng Lai, Wei-Ning Chen, Te-Cheng Hsu, Che Lin, Yu Tsao, Semon Wu
<span title="2020-03-13">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
With this clinical application in mind, we developed a deep neural network (DNN) combining heterogeneous data sources of gene expression and clinical data to accurately predict the overall survival of  ...  Then, by using a systems biology approach, prognosis relevance values (PRV) were then calculated to select eight additional novel prognostic gene biomarkers.  ...  The publication of this article was funded by Ministry of Science and Technology, Taiwan. Grant number is 108-2218-E-002-061-.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-61588-w">doi:10.1038/s41598-020-61588-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32170141">pmid:32170141</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aaueubzepvbspayjl3mth3mofy">fatcat:aaueubzepvbspayjl3mth3mofy</a> </span>
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Low Concordance between Gene Expression Signatures in ER Positive HER2 Negative Breast Carcinoma Could Impair Their Clinical Application

Enora Laas, Peter Mallon, Francois P. Duhoux, Amina Hamidouche, Roman Rouzier, Fabien Reyal, William B. Coleman
<span title="2016-02-19">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
We aim to evaluate prognostic concordance among eight gene expression signatures, on a large dataset of ER positive HER2 negative breast cancers.  ...  Numerous prognostic gene expression signatures have been recently described. Among the signatures there is variation in the constituent genes that are utilized.  ...  Similarly, the Her2 gene expression status was determined using the 216836_s_at probe set. A density plot of the 1,127 gene expression values showed a bimodal distribution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0148957">doi:10.1371/journal.pone.0148957</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26895349">pmid:26895349</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4760978/">pmcid:PMC4760978</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vvjh55sl5rc77o5wgtxbpfsteu">fatcat:vvjh55sl5rc77o5wgtxbpfsteu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011145200/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0148957&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/78/1c78c1879b3ad206073adebd03005240c7c6278a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0148957"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760978" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer

Andrew E Teschendorff, Ahmad Miremadi, Sarah E Pinder, Ian O Ellis, Carlos Caldas
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Furthermore, we show that the heterogeneity in clinical outcome of ERnegative breast cancer is related to the variability in expression levels of complement and immune response pathway genes, independent  ...  Moreover, we show that, in contrast to ER-positive tumours, the majority of prognostic markers in ER-negative breast cancer are over-expressed in the good prognosis group and are associated with activation  ...  We thank Ali Naderi for useful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-8-r157">doi:10.1186/gb-2007-8-8-r157</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17683518">pmid:17683518</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2374988/">pmcid:PMC2374988</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cphstvz755gtjbnb36khiipdne">fatcat:cphstvz755gtjbnb36khiipdne</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170818062555/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-8-r157?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/ec/37ece643b1d698800d969a3f9c10339b97f670be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-8-r157"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374988" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prostate cancer in young men represents a distinct clinical phenotype: gene expression signature to predict early metastases

Yuan C. Ding, Huiqing Wu, Elai Davicioni, R. Jeffrey Karnes, Eric A. Klein, Robert B. Den, Linda Steele, Susan L. Neuhausen
<span title="2021-03-09">2021</span> <i title="OAE Publishing Inc."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2dpi332yffz5g4b3tqqorfxoi" style="color: black;">Journal of Translational Genetics and Genomics</a> </i> &nbsp;
We measured genome-wide gene expression for 119 tumor and matched benign tissues from prostatectomies of men diagnosed at ≤ 50 years and > 70 years and identified age-related differentially expressed genes  ...  (DEGs) for tissue type and Gleason score.  ...  Acknowledgements The authors thank Charles Warden for downloading the decipher GRID data sets from the Decipher Biosciences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.20517/jtgg.2021.01">doi:10.20517/jtgg.2021.01</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33928239">pmid:33928239</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8081383/">pmcid:PMC8081383</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vt5urnubxjeiti5mcb33duj6oy">fatcat:vt5urnubxjeiti5mcb33duj6oy</a> </span>
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A network-based method for identifying prognostic gene modules in lung squamous carcinoma

Lin Feng, Run Tong, Xiaohong Liu, Kaitai Zhang, Guiqi Wang, Lei Zhang, Ning An, Shujun Cheng
<span title="2016-02-23">2016</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Using a network-based greedy searching algorithm to analyze the training cohort (n = 69) and three independent testing cohorts, we successfully identified a significant 22-gene module in which expression  ...  Differentially expressed genes with similar expression in precancerous and cancer samples were identified.  ...  Density curves of Pearson correlation in three stages. A bimodal distribution was seen for the developmental stage, in contrast to the unimodal distributions of the progression and cancer stages.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.7632">doi:10.18632/oncotarget.7632</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26919109">pmid:26919109</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4951267/">pmcid:PMC4951267</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kuhwfvsuu5bmxireezierll5wa">fatcat:kuhwfvsuu5bmxireezierll5wa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430062824/http://www.oncotarget.com/index.php?journal=oncotarget&amp;page=article&amp;op=download&amp;path%5B%5D=7632&amp;path%5B%5D=22120" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/1c/d21ccdecf5ee241acb52d43a1975a9a7b492a30f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.7632"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4951267" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A novel immuno-oncology algorithm measuring tumor microenvironment to predict response to immunotherapies

Tyler J. Nielsen, Brian Z. Ring, Robert S. Seitz, David R. Hout, Brock L. Schweitzer
<span title="2021-03-09">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ifjemtdanzevfbtz3nv7p24qjm" style="color: black;">Heliyon</a> </i> &nbsp;
We developed an algorithm optimized for genes expressed in the mesenchymal and immunomodulatory subtypes of a 101-gene triple negative breast cancer model (Ring, BMC Cancer, 2016, 16:143) as a means to  ...  We compared the outcome of the algorithm (IO score) with the 101-gene model and found 88% concordance, indicating the models are correlated but not identical, and may be measuring different TME features  ...  Acknowledgements The authors are grateful to Linda Kahl for editorial assistance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.heliyon.2021.e06438">doi:10.1016/j.heliyon.2021.e06438</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33748492">pmid:33748492</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7970145/">pmcid:PMC7970145</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fd7hnufsu5dqjd3wj3qff2ytdi">fatcat:fd7hnufsu5dqjd3wj3qff2ytdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210602221305/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7970145&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/15/bc/15bcd2df2bd153ea9f6439f6e51dd70a8fbd6e5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.heliyon.2021.e06438"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970145" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data

Laurence de Torrenté, Samuel Zimmerman, Masako Suzuki, Maximilian Christopeit, John M. Greally, Jessica C. Mar
<span title="2020-12-28">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results Surprisingly, the expression of less than 50% of all genes was Normally-distributed, with other distributions including Gamma, Bimodal, Cauchy, and Lognormal also represented.  ...  Our study investigated the prevalence of a range of gene expression distributions in three different tumor types from the Cancer Genome Atlas (TCGA).  ...  Acknowledgements We thank Milos Tanurdzic, Mark Donoghue and Deanne Taylor for useful discussion of this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03892-w">doi:10.1186/s12859-020-03892-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33371881">pmid:33371881</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qqph457b6vdapln5pue72txnhq">fatcat:qqph457b6vdapln5pue72txnhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210227095917/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03892-w.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cd/57/cd57ec1da3c15cc76b0ef1a8d5624da4f617bc51.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03892-w"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Ep-CAM RNA expression predicts metastasis-free survival in three cohorts of untreated node-negative breast cancer

Marcus Schmidt, Ilka Brigitte Petry, Daniel Böhm, Antje Lebrecht, Christian von Törne, Susanne Gebhard, Aslihan Gerhold-Ay, Cristina Cotarelo, Marco Battista, Wiebke Schormann, Evgenia Freis, Silvia Selinski (+7 others)
<span title="2010-03-30">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leczobeksfd3pe5z3xcrxwb2jy" style="color: black;">Breast Cancer Research and Treatment</a> </i> &nbsp;
Ep-CAM RNA expression predicts metastasis-free survival in three cohorts of untreated node-negative breast cancer.  ...  Acknowledgment: This study was supported by the BMBF (NGFN project Oncoprofile). We thank Ms. Susanne Lindemann for competent bibliographic assistance.  ...  Although the highest and lowest scores were associated with high and low RNA expression no correlation was seen for the intermediate scores.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10549-010-0856-5">doi:10.1007/s10549-010-0856-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20352488">pmid:20352488</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mqywyhuhxzg4ffrm2kpa2fpn7q">fatcat:mqywyhuhxzg4ffrm2kpa2fpn7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726201819/https://hal.archives-ouvertes.fr/hal-00561313/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/e9/e1e98692fb3d7cfc44e59e195bdbb472ffca1cea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10549-010-0856-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Methylation-To-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, And Pathologic Complete Response in Multiple Cohorts [article]

Jeffrey Ahearn Thompson, Brock C. Christensen, Carmen J. Marsit
<span title="2017-09-12">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
scores for overall survival, distant metastasis, and chemosensitivity.  ...  Methods: Gene expression and DNA methylation values as well as clinical variables were integrated via M2EFM to build prognostic models of overall survival using 1028 breast tumor samples and further applied  ...  Large scale collection of cancer genomic data, such as The Cancer Genome Atlas (TCGA) (2) and the International Cancer Genome Consortium (3) , and expression repositories such as NCBI's Gene Expression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/187526">doi:10.1101/187526</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ltnvejkzgvgg3brcnftiv5qzwy">fatcat:ltnvejkzgvgg3brcnftiv5qzwy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427141140/https://www.biorxiv.org/content/biorxiv/early/2017/09/12/187526.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/4b/704b4c3a613e67113753ac263bb086a3ffcc1f4c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/187526"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The 3′UTR signature defines a highly metastatic subgroup of triple-negative breast cancer

Lei Wang, Xin Hu, Peng Wang, Zhi-Ming Shao
<span title="2016-08-01">2016</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Time-dependent ROC comparisons and Kaplan-Meier analyses confirmed an outstanding discriminating power of our prognostic model for TNBC patients.  ...  We collected 327 publicly available microarrays and generated the 3′UTR landscape based on expression ratios of alternative 3′UTR.  ...  GRANT SUPPORT This work was supported by grants from the Shanghai Committee of Science and Technology, China (12DZ2260100) and the National Natural Science Foundation of China (31271413, 81602316).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.10975">doi:10.18632/oncotarget.10975</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27494850">pmid:27494850</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5312352/">pmcid:PMC5312352</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/enham27avvgabbicvqesabha3m">fatcat:enham27avvgabbicvqesabha3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228125420/http://pdfs.semanticscholar.org/9241/298c3cfe24907d7fec1315aa28a55da9fd9a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.10975"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312352" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

Denise M. Wolf, Marc E. Lenburg, Christina Yau, Aaron Boudreau, Laura J. van 't Veer, Benjamin Haibe-Kains
<span title="2014-02-07">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Overall, co-expression modules provide a high-level functional view of breast cancer that complements the "cancer hallmarks" and may form the basis for improved predictors and treatments.  ...  Per dataset, we identified genes with bimodal expression and used mixturemodel clustering to ultimately define 11 modules of genes that are consistently co-regulated across multiple datasets.  ...  Acknowledgments We would like to thank the women who participated in the clinical trials represented in the datasets we analyzed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0088309">doi:10.1371/journal.pone.0088309</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24516633">pmid:24516633</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3917875/">pmcid:PMC3917875</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gf5wjcojcjgtvh27b6txk4aa6a">fatcat:gf5wjcojcjgtvh27b6txk4aa6a</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3917875/PMC3917875-journal.pone.0088309.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/03/3d/033d81da7d1262cbd5e48b0357744a4b98aa3429.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0088309"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917875" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts

Jeffrey A. Thompson, Brock C. Christensen, Carmen J. Marsit
<span title="2018-03-26">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
scores for overall survival, distant metastasis, and chemosensitivity.  ...  Methods : Gene expression and DNA methylation values as well as clinical variables were integrated via M2EFM to build prognostic models of overall survival using 1028 breast tumor samples and further applied  ...  Large scale collection of cancer genomic data, such as The Cancer Genome Atlas (TCGA) (2) and the International Cancer Genome Consortium (3) , and expression repositories such as NCBI's Gene Expression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-23494-0">doi:10.1038/s41598-018-23494-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29581450">pmid:29581450</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5979962/">pmcid:PMC5979962</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2f4thgrqvfbrnfg2fahsowxz34">fatcat:2f4thgrqvfbrnfg2fahsowxz34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723093928/https://www.biorxiv.org/content/biorxiv/early/2017/09/12/187526.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/76/1c76aac91a20a660081cc30491ef6b8b45b1c16e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-23494-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979962" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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