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PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer

Andrew E. Teschendorff, Ali Naderi, Nuno L. Barbosa-Morais, Carlos Caldas
2006 Computer applications in the biosciences : CABIOS  
We validate our methodology using six independent datasets by rediscovering major classifiers in ER negative and ER positive breast cancer and in prostate cancer.  ...  Motivation: Elucidating the molecular taxonomy of cancers and finding biological and clinical markers from microarray experiments is problematic due to the large number of variables being measured.  ...  Depending on the application it can be used to either find major molecular classifiers, or genes defining small outlier subgroups, or simply as a filtering step prior to supervised analysis to remove likely  ... 
doi:10.1093/bioinformatics/btl174 pmid:16682424 fatcat:mfmh3vkpwjgotmp6p7eigmugre

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
2007 Genome Biology  
Breast cancer prognosis A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor-negative  ...  Results: We apply a recently proposed feature selection method in an integrative analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in ER-negative  ...  Acknowledgements This research was supported by grants from Cancer Research UK. We thank Ali Naderi for useful discussions.  ... 
doi:10.1186/gb-2007-8-8-r157 pmid:17683518 pmcid:PMC2374988 fatcat:cphstvz755gtjbnb36khiipdne

Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine

Zhou Zhu, Nathan T. Ihle, Paul A. Rejto, Patrick P. Zarrinkar
2016 BMC Genomics  
Results: Genes with outlier features are strongly and specifically enriched with those known to be associated with cancer and relevant biological processes, despite no a priori knowledge being used to  ...  We thus introduce a complementary data mining strategy to identify genes with exceptional sensitivity in subsets, or outlier groups, of cell lines, allowing an unbiased analysis without any a priori assumption  ...  Acknowledgements We are grateful to Jarek Kostrowicki, Darwin Lee, Kim Arndt, Valeria Fantin, Sapna Vijayakumar, Keith Ching, Shibing Deng, Yu Jean Wang, Pete Olson and Todd VanArsdale for sharing their  ... 
doi:10.1186/s12864-016-2807-y pmid:27296290 pmcid:PMC4907009 fatcat:ju3bfqgr6rhuzcix3ciniphufa

Intratumoral and peritumoral radiomics for the pretreatment prediction of pathological complete response to neoadjuvant chemotherapy based on breast DCE-MRI

Nathaniel M. Braman, Maryam Etesami, Prateek Prasanna, Christina Dubchuk, Hannah Gilmore, Pallavi Tiwari, Donna Plecha, Anant Madabhushi
2017 Breast Cancer Research  
In this study, we evaluated the ability of radiomic textural analysis of intratumoral and peritumoral regions on pretreatment breast cancer dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI  ...  Feature selection was used to identify a set of top pCR-associated features from within a training set (n = 78), which were then used to train multiple machine learning classifiers to predict the likelihood  ...  Acknowledgements The authors thank Elena DuPont for her support in the organization and transfer of patient data.  ... 
doi:10.1186/s13058-017-0846-1 pmid:28521821 pmcid:PMC5437672 fatcat:q3uqysclgjf6xh5u4evwv7ipva

PADGE: analysis of heterogeneous patterns of differential gene expression

Li Li, Amitabha Chaudhuri, John Chant, Zhijun Tang
2007 Physiological Genomics  
ACKNOWLEDGMENTS We thank Tom Wu for insightful discussion, Xiaolong Yu for suggestions and help with statistical analysis, Kenneth Jung for implementation of CyberT, and William Wood and Zemin Zhang for  ...  Recently, two methods, cancer outlier profile analysis (COPA) (12) and profile analysis using clustering and kurtosis (PACK) (11) , were developed to identify cancer markers within tumor subclasses  ...  outlier profile analysis (COPA), and kurtosis (Kurt).  ... 
doi:10.1152/physiolgenomics.00259.2006 pmid:17925482 fatcat:oh7ak2w6h5hl7kluk5ctmiroge

The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data

Jing Wang, Sijin Wen, W Fraser Symmans, Lajos Pusztai, Kevin R Coombes
2009 Cancer Informatics  
We carried out simulation studies and applied the method to real data from a cancer gene expression profiling study.  ...  In practice, however, BIC appears to be overly sensitive and may lead to the identification of bimodally expressed genes that are unreliable or not clinically useful.  ...  This step is the same as the model-based-clustering technique. (2) Using kurtosis to characterize features and find relevant classifiers.  ... 
pmid:19718451 pmcid:PMC2730180 fatcat:mmdgr7ofvnfxnlqtoymqjb7l3q

Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology

Lokman Cevik, Marilyn Vazquez Landrove, Mehmet Tahir Aslan, Vasilii Khammad, Francisco Jose Garagorry Guerra, Yolanda Cabello‐Izquierdo, Wesley Wang, Jing Zhao, Aline Paixao Becker, Catherine Czeisler, Anne Costa Rendeiro, Lucas Luis Sousa Véras (+14 others)
2022 Brain Pathology  
We used simple information theory calculations on a brain cancer simulation model and real-world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information  ...  Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH-mutant tumors  ...  The authors have no conflicts of interest to declare that are relevant to the content of this article.  ... 
doi:10.1111/bpa.13050 pmid:35014126 pmcid:PMC9425010 fatcat:l3pkltijkfejvittzkt6euhsg4

Imaging genotyping of functional signaling pathways in lung squamous cell carcinoma using a radiomics approach

So Hyeon Bak, Hyunjin Park, Ho Yun Lee, Youngwook Kim, Hyung-Lae Kim, Sin-Ho Jung, Hyeseung Kim, Jonghoon Kim, Keunchil Park
2018 Scientific Reports  
We aimed to identify predictive imaging biomarkers that underpin genomic alterations and clinical outcomes in lung squamous cell carcinoma (SQCC) using a radiomics approach.  ...  Mutational profiles for core signaling pathways of lung SQCC were classified into five categories: redox stress, apoptosis, proliferation, differentiation, and chromatin remodelers.  ...  Acknowledgements The authors of this manuscript declare no relationships with any companies whose products or services may be related to the subject matter of the article.  ... 
doi:10.1038/s41598-018-21706-1 pmid:29459639 pmcid:PMC5818618 fatcat:pf3db2simzhspogydsbfvomqq4

Prognostic immune-related gene models for breast cancer: a pooled analysis

Jianli Zhao, Ying Wang, Zengding Lao, Siting Liang, Jingyi Hou, Yunfang Yu, Herui Yao, Na You, Kai Chen
2017 OncoTargets and Therapy  
This model employed a methodology called profile analysis using clustering and kurtosis (PACK). PACK was a semi-supervised algorithm, consisting of two main steps.  ...  These findings may be due to increases in cytotoxic immune cell infiltrates in these tumors.  ...  Disclosure The authors report no conflicts of interest in this work.  ... 
doi:10.2147/ott.s144015 pmid:28979134 pmcid:PMC5602680 fatcat:fuwylj5tarhwtny4jcd7multsa

Glioma Grading via Analysis of Digital Pathology Images Using Machine Learning

Saima Rathore, Tamim Niazi, Muhammad Aksam Iftikhar, Ahmad Chaddad
2020 Cancers  
Cancer pathology reflects disease progression (or regression) and associated molecular characteristics, and provides rich phenotypic information that is predictive of cancer grade and has potential implications  ...  We sought to evaluate the combined effect of conventional imaging, clinical, and texture features by assessing the predictive value of each feature type and their combinations through a predictive classifier  ...  A SVM classifier [29] with linear kernel was used to predict the cancer grade.  ... 
doi:10.3390/cancers12030578 pmid:32131409 pmcid:PMC7139732 fatcat:7cug7wzk2vchjou4vulngbyi3e

A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma

Daniel G. Piqué, Cristina Montagna, John M. Greally, Jessica C. Mar
2019 British Journal of Cancer  
Oncogenes promote the development of therapeutic targets against subsets of cancers. Only several hundred oncogenes have been identified, primarily via mutation-based approaches, in the human genome.  ...  We thank the Molecular Cytogenetics Core at the Albert Einstein College of Medicine-in particular, Dr. Jidong Shan and Dr. Yinghui Song-for assisting with the CBX2 silencing studies.  ...  ACKNOWLEDGEMENTS Samuel Zimmerman and Associate Prof. Tao Wang provided advice regarding bioinformatics pipelines and analysis.  ... 
doi:10.1038/s41416-019-0387-8 pmid:30820027 pmcid:PMC6462018 fatcat:ebjdrvwwsnd4fncdruxlezazci

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Adam Abeshouse, Clement Adebamowo, Sally N. Adebamowo, Rehan Akbani, Teniola Akeredolu, Adrian Ally, Matthew L. Anderson, Pavana Anur, Elizabeth L. Appelbaum, Joshua Armenia, J. Todd Auman, Matthew H. Bailey (+252 others)
2017 Cell  
to other cancer types.  ...  diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and  ...  Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling. Oncogene 29, 845-854.  ... 
doi:10.1016/j.cell.2017.10.014 pmid:29100075 pmcid:PMC5693358 fatcat:xq7ald3qf5fixolsmscmuda2yq

Detection of Patient Subgroups with Differential Expression in Omics Data: A Comprehensive Comparison of Univariate Measures

Maike Ahrens, Michael Turewicz, Swaantje Casjens, Caroline May, Beate Pesch, Christian Stephan, Dirk Woitalla, Ralf Gold, Thomas Brüning, Helmut E. Meyer, Jörg Rahnenführer, Martin Eisenacher (+1 others)
2013 PLoS ONE  
ROC curve analysis and AUC values are used to quantify the ability of the methods to distinguish between genes or proteins with and without certain subgroup patterns.  ...  Detection of yet unknown subgroups showing differential gene or protein expression is a frequent goal in the analysis of modern molecular data.  ...  For the above mentioned reasons, we focus on univariate methods and do not consider COPA in our work [5] . proposed a two-step procedure called profile analysis using clustering and kurtosis (PACK), which  ... 
doi:10.1371/journal.pone.0079380 pmid:24278130 pmcid:PMC3838370 fatcat:a52jzo5rwrbrbpbhqyhv5r4x5u

Human Ovarian Cancer Tissue Exhibits Increase of Mitochondrial Biogenesis and Cristae Remodeling

Anna Signorile, Domenico De Rasmo, Antonella Cormio, Clara Musicco, Roberta Rossi, Francesco Fortarezza, Luigi Leonardo Palese, Vera Loizzi, Leonardo Resta, Giovanni Scillitani, Ettore Cicinelli, Francesca Simonetti (+4 others)
2019 Cancers  
Statistical analysis was performed using Student's t-test, Mann-Whitney U test, and principal component analysis (PCA).  ...  Ovarian cancer (OC) is the most lethal gynecologic cancer characterized by an elevated apoptosis resistance that, potentially, leads to chemo-resistance in the recurrent disease.  ...  Pacelli, and R. Scrima for critical discussion and P. Lattanzio for sample collection and storage. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers11091350 pmid:31547300 pmcid:PMC6770021 fatcat:bbvkcaxzenh2vm37k66tjvlefu

How clinical imaging can assess cancer biology

Roberto García-Figueiras, Sandra Baleato-González, Anwar R. Padhani, Antonio Luna-Alcalá, Juan Antonio Vallejo-Casas, Evis Sala, Joan C. Vilanova, Dow-Mu Koh, Michel Herranz-Carnero, Herbert Alberto Vargas
2019 Insights into Imaging  
This paper aims to summarize the current and emerging applications of imaging in tumor biology assessment.  ...  However, cancers usually exhibit characteristic structural, physiologic, and molecular features and display specific biological capabilities named hallmarks.  ...  These findings were secondary to the predominance of fibrosis within the lesion. b Histological analysis (H&E, × 20) confirmed an abundant tumor desmoplastic reaction (asterisks) with clusters of tumor  ... 
doi:10.1186/s13244-019-0703-0 pmid:30830470 pmcid:PMC6399375 fatcat:tjs7aap3kjhpjk3xfgmmp3byxu
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