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Bayesian Mixture Models For Gene Expression And Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, Jeffrey S. Morris Mar 2006

Bayesian Mixture Models For Gene Expression And Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, Jeffrey S. Morris

Jeffrey S. Morris

We review the use of semi-parametric mixture models for Bayesian inference in high throughput genomic data. We discuss three specific approaches for microarray data, for protein mass spectrometry experiments, and for SAGE data. For the microarray data and the protein mass spectrometry we assume group comparison experiments, i.e., experiments that seek to identify genes and proteins that are differentially expressed across two biologic conditions of interest. For the SAGE data example we consider inference for a single biologic sample.


Analysis Of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, Kevin R. Coombes Mar 2006

Analysis Of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

In this chapter, we demonstrate how to analyze MALDI-TOF/SELDITOF mass spectrometry data using the wavelet-based functional mixed model introduced by Morris and Carroll (2006), which generalizes the linear mixed models to the case of functional data. This approach models each spectrum as a function, and is very general, accommodating a broad class of experimental designs and allowing one to model nonparametric functional effects for various factors, which can be conditions of interest (e.g. cancer/normal) or experimental factors (blocking factors). Inference on these functional effects allows us to identify protein peaks related to various outcomes of interest, including ...


On The Robustness Of Robustness Checks Of The Environmental Kuznets Curve, Marzio Galeotti, Matteo Manera, Alessandro Lanza Jan 2006

On The Robustness Of Robustness Checks Of The Environmental Kuznets Curve, Marzio Galeotti, Matteo Manera, Alessandro Lanza

Matteo Manera

Since its first inception in the debate on the relationship between environment and growth in 1992, the Environmental Kuznets Curve has been subject of continuous and intense scrutiny. The literature can be roughly divided in two historical phases. Initially, after the seminal contributions, additional work aimed to extend the investigation to new pollutants and to verify the existence of an inverted-U shape as well as assessing the value of the turning point. The following phase focused instead on the robustness of the empirical relationship, particularly with respect to the omission of relevant explanatory variables other than GDP, alternative datasets, functional ...


Improved Peak Detection And Quantification Of Mass Spectrometry Data Acquired From Surface-Enhanced Laser Desorption And Ionization By Denoising Spectra With The Undecimated Discrete Wavelet Transform, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, Henry M. Kuerer Dec 2005

Improved Peak Detection And Quantification Of Mass Spectrometry Data Acquired From Surface-Enhanced Laser Desorption And Ionization By Denoising Spectra With The Undecimated Discrete Wavelet Transform, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, Henry M. Kuerer

Jeffrey S. Morris

Background: Mass spectrometry, especially surface enhanced laser desorption and ionization (SELDI) is increasingly being used to find disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids such as serum, urine, or nipple aspirate fluid. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. For example, Yasui and colleagues opted to replace continuous measures of the size of a peak by a simple binary indicator of its presence or absence in their analysis of a set of spectra from prostate cancer patients.

Methods: We collected nipple ...


Pooling Information Across Different Studies And Oligonucleotide Microarray Chip Types To Identify Prognostic Genes For Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, Li Zhang Dec 2005

Pooling Information Across Different Studies And Oligonucleotide Microarray Chip Types To Identify Prognostic Genes For Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, Li Zhang

Jeffrey S. Morris

Our goal in this work is to pool information across microarray studies conducted at different institutions using two different versions of Affymetrix chips to identify genes whose expression levels offer information on lung cancer patients’ survival above and beyond the information provided by readily available clinical covariates. We combine information across chip types by identifying “matching probes” present on both chips, and then assembling them into new probesets based on Unigene clusters. This method yields comparable expression level quantifications across chips without sacrificing much precision or significantly altering the relative ordering of the samples. We fit a series of multivariable ...


Serum Proteomics Profiling: A Young Technology Begins To Mature, Kevin R. Coombes, Jeffrey S. Morris, Jianhua Hu, Sarah R. Edmondson, Keith A. Baggerly Mar 2005

Serum Proteomics Profiling: A Young Technology Begins To Mature, Kevin R. Coombes, Jeffrey S. Morris, Jianhua Hu, Sarah R. Edmondson, Keith A. Baggerly

Jeffrey S. Morris

No abstract provided.


Signal In Noise: Evaluating Reported Reproducibility Of Serum Proteomic Tests For Ovarian Cancer, Keith A. Baggerly, Jeffrey S. Morris, Sarah R. Edmonson, Kevin R. Coombes Feb 2005

Signal In Noise: Evaluating Reported Reproducibility Of Serum Proteomic Tests For Ovarian Cancer, Keith A. Baggerly, Jeffrey S. Morris, Sarah R. Edmonson, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profi ling of serum initially appeared to be dramatically effective for diagnosis of early-stage ovarian cancer, but these results have proven diffi cult to reproduce. A recent publication reported good classifi cation in one dataset using results from training on a much earlier dataset, but the authors have since reported that they did not perform the analysis as described. We examined the reproducibility of the proteomic patterns across datasets in more detail. Our analysis reveals that the pattern that enabled successful classifi cation is biologically implausible and that the method, properly applied, does not classify the data accurately. We ...


High-Resolution Serum Proteomic Patterns For Ovarian Cancer Detection, Keith A. Baggerly, Sarah R. Edmonson, Jeffrey S. Morris, Kevin R. Coombes Nov 2004

High-Resolution Serum Proteomic Patterns For Ovarian Cancer Detection, Keith A. Baggerly, Sarah R. Edmonson, Jeffrey S. Morris, Kevin R. Coombes

Jeffrey S. Morris

No abstract provided.


Quality Control And Peak Finding For Proteomics Data Collected From Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption And Ionization., Jeffrey S. Morris, Kevin R. Coombes, Herbert A. Fritsche, Charlotte Clarke, Jeng-Neng Chen, Keith A. Baggerly, Lian-Chun Xiao, Mien-Chie Hung, Henry M. Kuerer Oct 2003

Quality Control And Peak Finding For Proteomics Data Collected From Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption And Ionization., Jeffrey S. Morris, Kevin R. Coombes, Herbert A. Fritsche, Charlotte Clarke, Jeng-Neng Chen, Keith A. Baggerly, Lian-Chun Xiao, Mien-Chie Hung, Henry M. Kuerer

Jeffrey S. Morris

Background: Recently, researchers have been using mass spectroscopy to study cancer. For use of proteomics spectra in a clinical setting, stringent quality-control procedures will be needed.

Methods: We pooled samples of nipple aspirate fluid from healthy breasts and breasts with cancer to prepare a control sample. Aliquots of the control sample were used on two spots on each of three IMAC ProteinChip® arrays (Ciphergen Biosystems, Inc.) on 4 successive days to generate 24 SELDI spectra. In 36 subsequent experiments, the control sample was applied to two spots of each ProteinChip array, and the resulting spectra were analyzed to determine how ...


A Comprehensive Approach To The Analysis Of Maldi-Tof Proteomics Spectra From Serum Samples., Keith A. Baggerly, Jeffrey S. Morris, Jing Wang, David Gold, Lian-Chun Xiao, Kevin R. Coombes Jun 2003

A Comprehensive Approach To The Analysis Of Maldi-Tof Proteomics Spectra From Serum Samples., Keith A. Baggerly, Jeffrey S. Morris, Jing Wang, David Gold, Lian-Chun Xiao, Kevin R. Coombes

Jeffrey S. Morris

For our analysis of the data from the First Annual Proteomics Data Mining Conference, we attempted to discriminate between 24 disease spectra (group A) and 17 normal spectra (group B). First, we processed the raw spectra by (i) correcting for additive sinusoidal noise (periodic on the time scale) affecting most spectra, (ii) correcting for the overall baseline level, (iii) normalizing, (iv) recombining fractions, and (v) using variable- width windows for data reduction. Also, we identified a set of polymeric peaks (at multiples of 180.6 Da) that is present in several normal spectra (B1–B8). After data processing, we found ...


Bayesian Shrinkage Estimation Of The Relative Abundance Of Mrna Transcripts Using Sage, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes Mar 2003

Bayesian Shrinkage Estimation Of The Relative Abundance Of Mrna Transcripts Using Sage, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

Serial analysis of gene expression (SAGE) is a technology for quantifying gene expression in biological tissue that yields count data that can be modeled by a multinomial distribution with two characteristics: skewness in the relative frequencies and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample may fail to capture a large number of expressed mRNA species present in the tissue. Empirical estimators of mRNA species’ relative abundance effectively ignore these missing species, and as a result tend to overestimate the abundance of the scarce observed species comprising a vast majority of ...


The Press For Help Project Concept, Program And Working Paper Of Emmanuel Mario B Santos And His Marc Guerrero Communications Inc., Emmanuel Mario B. Santos Aka Marc Guerrero Jan 2003

The Press For Help Project Concept, Program And Working Paper Of Emmanuel Mario B Santos And His Marc Guerrero Communications Inc., Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

FORETHOUGHT. DECLARATION OF IDEAOLOGY AND PRINCIPLES. VISION. MISSION. VALUES. GOALS. BASIC HELP project. EDUCATIONAL HELP project. MEDICAL HELP project. LEGAL HELP project. EMERGENCY HELP project. LIVELIHOOD HELP project. SPIRITUAL and CULTURAL HELP project. ENVIRONMENTAL HELP project. REENGINEERING HELP project. INTERNATIONAL HELP project. QUADRO CREDO Matthew 5.1-12, the Jerusalem Bible. The Universal Filipino Beatitudes. SALIN SA FILIPINO. DESIDERATA. AFTERTHOUGHT.


Intracellular Coexpression Of Epidermal Growth Factor Receptor, Her-2/Neu, And P21ras In Human Breast Cancers: Evidence For The Existence Of Distinctive Patterns Of Genetic Evolution That Are Common To Tumors From Different Patients, Stanley E. Shackney, Agnese A. Pollice, Charles A. Smith, Laura E. Janocko, Lillian Sweeney, Kathryn A. Brown, Sarita G. Singh, Lingping Gu, Robert Yakulis, Joseph F. Lucke Jan 1998

Intracellular Coexpression Of Epidermal Growth Factor Receptor, Her-2/Neu, And P21ras In Human Breast Cancers: Evidence For The Existence Of Distinctive Patterns Of Genetic Evolution That Are Common To Tumors From Different Patients, Stanley E. Shackney, Agnese A. Pollice, Charles A. Smith, Laura E. Janocko, Lillian Sweeney, Kathryn A. Brown, Sarita G. Singh, Lingping Gu, Robert Yakulis, Joseph F. Lucke

Joseph Lucke

Multiparameter flow cytometry studies were performed on cells from the primary tumors of 94 patients with breast cancer. Correlated cellular measurements of cell DNA content, Her-2/neu, epidermal growth factor receptor (EGFR), and p21ras levels were performed on each of 5,000 to 100,000 cells from each tumor. When criteria for positivity were matched with those in common use for immunohistochemical studies, 28 of 94 (30\%) breast cancers were classified as positive for Her-2/neu overexpression. When similar criteria were applied to the EGFR measurements, 23 of 94 (24\%) cases were classified as positive for EGFR overexpression. Similarly, 23 ...


Assessing Sequential Oncogene Amplification In Human Breast Cancer, Laura E. Janocko, Joseph F. Lucke, David W. Groft, Kathryn A. Brown, Charles A. Smith, Agnese A. Pollice, Sarita G. Singh, Robert Yakulis, Robert J. Hartsock, Stanley E. Shackney Jan 1995

Assessing Sequential Oncogene Amplification In Human Breast Cancer, Laura E. Janocko, Joseph F. Lucke, David W. Groft, Kathryn A. Brown, Charles A. Smith, Agnese A. Pollice, Sarita G. Singh, Robert Yakulis, Robert J. Hartsock, Stanley E. Shackney

Joseph Lucke

Studies of amplification and/or overexpression of c-myc, HER-2/neu, and H-ras in breast cancer have shown that each is associated with a poor prognosis. The purpose of this study was to explore the possibility that there is a preferred sequence of amplification of these oncogenes in breast cancer. The frequencies of amplification and patterns of co-amplification of c-myc, HER-2/neu, and H-ras were studied in a group of 84 breast cancers. The data suggested a preferred sequence of amplification that consisted of c-myc amplification-HER-2/neu amplification-H-ras amplification. This model was supported by loglinear analysis. In addition, the levels of ...