Penalized orthogonal-components regression for large p small n data

03 Mar. 2010 | Publications | Contributor(s): Min Zhang, Dabao Zhang

Here we propose a penalized orthogonal-components regression (POCRE) for large p small n data. Orthogonal components are sequentially constructed to maximize, upon standardization, their correlation to the re-sponse residuals. A new penalization framework, implemented via empirical Bayes …

Simultaneous genome-wide association studies of anti-cyclic citrullinated peptide in rheumatoid arthritis using penalized orthogonal-components regression

03 Mar. 2010 | Publications | Contributor(s): Min Zhang, Dabao Zhang

Genome-wide associations between single-nucleotide polymorphisms and clinical traits were simultaneously conducted using penalized orthogonal-components regression. This method was developed to identify the genetic variants controlling phenotypes from a massive number of candidate variants. By …

Case-control genome-wide association study of rheumatoid arthritis from Genetic Analysis Workshop 16 using penalized orthogonal-components regression-linear discriminant analysis

03 Mar. 2010 | Publications | Contributor(s): Dabao Zhang, Min Zhang

Currently, genome-wide association studies (GWAS) are conducted by collecting a massive number of SNPs (i.e., large p) for a relatively small number of individuals (i.e., small n) and associations are made between clinical phenotypes and genetic variation one single-nucleotide polymorphism (SNP) at …

Browse Tool Output Collections

16 Dec. 2009 | Tools | Contributor(s): Ann Christine Catlin

Browse Tool Output Collections

Pattern Recognition for Normalized LC-MS Data

01 Jul. 2009 | Tools | Contributor(s): Ann Christine Catlin, George Howlett

This tool provides principal component analysis (PCA), linear discriminate analysis (LDA), and canonical discriminate analysis (CDA) for data clustering on aligned, normalized LC-MS datasets.

Peak Alignment of LC-MS Data

24 Jun. 2009 | Tools | Contributor(s): Ann Christine Catlin, George Howlett

Peak alignment addresses retention time shift by recongnizing and aligning significant peaks; it then uses discrete deconvolution to align overlapped peaks.

Significance Testing of Normalized LC-MS Data

23 Jun. 2009 | Tools | Contributor(s): Ann Christine Catlin

Several statistical significance tests are employed to identify peptide or metabolite peaks that either make significant contributions to the molecular profile of a sample or distinguish a group of samples from others.

Normalization of Aligned LC-MS Data

18 Jun. 2009 | Tools | Contributor(s): Ann Christine Catlin, George Howlett

Normalization attempts to quantitatively filter overall peak intensity variations due to experiment errors such as systematic variable injection volumes loaded onto LC-MS.

The Purdue Proteome Discovery Pipeline

16 Jun. 2009 | Series | Contributor(s): Ann Christine Catlin, George Howlett

The Proteome Discovery Pipeline (PDP) is a data analysis system for mass spectrometry-based proteomics which was developed through the collaborative research efforts of the Bindley Biosciences Center, the Cyber Center and the eEnterprise Center at Purdue University. The PDP offers a data analysis …

Workspace

27 Apr. 2009 | Tools | Contributor(s): Nicholas Kisseberth

Workspace

Photocleavable peptide biosensors for detecting intracellular kinase activity.

20 Apr. 2009 | Online Presentations | Contributor(s): Ekaterina A. Placzek

The primary goal of our research is to investigate the development and progression of chronic myeloid leukaemia (CML). CML results from translocation of chromosomes 9 and 22 and yields an unregulated Break-Point-Cluster-Abelson (Bcr-Abl) mutant kinase. The Bcr-Abl protein signalling then leads to …

Building a Data Support Infrastructure for the Cancer Care Engineering OMIC Study

10 Apr. 2009 | Teaching Materials | Contributor(s): Ann Christine Catlin

OMIC profiles hold enormous promise for transforming our understanding of biological processes and revealing the underlying biological mechanisms, especially the functional and interactive networks contributing to complex biological systems. Rapid advances in large scale OMIC analyses have produced …

PCTX and N2A Image slide show

18 Mar. 2009 | Downloads | Contributor(s): Stephanie Kidd, Laurie Parker

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OMIC Explorer

16 Mar. 2009 | Tools | Contributor(s): Philip Livengood

Visual exploration of GCxGC MS Data

An Adaptive-Predictive Model for Colonic Neoplasia Incidence

15 Mar. 2009 | Downloads | Contributor(s): Eric Sherer

Discovery Brown Bag Seminar Series sponsored by Regenstrief Center for Healthcare Engineering. RCHE presents Dr. Eric Sherer, Medical Informatics Fellow Candidate, VA CIEBP. Dr. Sherer has contributed several population-based models to cceHUB, and interested users can explore the colorectal cancer …

L. Parker talk at US-HUPO

02 Mar. 2009 | Online Presentations | Contributor(s): Laurie Parker

This is a 10-minute talk I gave at the US-HUPO meeting on Feb. 23rd, 2009 in the "Chemical Proteomics" session. It describes the essentials of our lab technology making artificial kinase substrates.

OMIC Data Formats: Notes for the Modeling Research Group

20 Feb. 2009 | Notes | Contributor(s): Ann Christine Catlin

Each OMIC analysis laboratory has one or more analysis workflows that begin with instrument-generated datasets, where the format of the instrument dataset made available to modeling researchers for analysis depends on the instrument, the analysis mode, and the available file conversion software. …

Global Proteomics Workflows at Bindley Biosciences Center

14 Feb. 2009 | Notes

The slides diagram the global proteomics workflows at Bindley Biosciences.

XCT PLUS: Agilent 1100 Series HPLC-Chip/MS System

14 Feb. 2009 | Notes

Nanospray LC/MS is well established as state-of-the-art technology because of its high sensitivity and low sample consumption. It is most often used for applications with limited sample amounts or when there is a need for analysis of trace level components in complex mixtures. Although nanospray …

Data Mining Approach: Global Proteomics for Cancer Care Engineering

14 Feb. 2009 | Notes | Contributor(s): Catherine Riley

The Proteomics Discovery Pipeline (PDP) bioinformatics infrastructure created at the Bindley Bioscience Center (at Purdue University) will be used for data management and data mining.

XCT PLUS Instrument Setup: Global Proteomics for Cancer Care Engineering

13 Feb. 2009 | Notes

The document describes the instrument setup for the XCT PLUS ESI ion trap located in the Bindley Biosciences Center at Purdue University. Laboratory analysis for global proteomics research is carried out by Jiri Adamec and Paige Riley. The sample preparation protocol describes the metholodology for …

Sample Preparation Protocol: Global Proteomics for Cancer Care Engineering

13 Feb. 2009 | Notes | Contributor(s): Catherine Riley

The urea-based trypsin digestion sample preparation protocol is used for the plasma samples acquired through the Cancer Care Engineering Colorectal Cancer OMIC Pilot Study. Prepared samples are analyzed using the XCT PLUS ESI ion trap located in the Bindley Biosciences Center at Purdue University.

LECO GC-TOF Instrument Setup: Metabolomics for Cancer Care Engineering

13 Feb. 2009 | Notes | Contributor(s): Daniel Raftery

This document describes the setup for the LECO GC-TOF mass spectrometry instrument in preparation for metabolomics GCxGC-MS analysis of serum samples processed from patient whole blood at the IUSCC clinic and transferred to the Raftery Metabolomics Analysis Laboratory. See also Metabolics GCxGC …

Sample Preparation : Metabolomics Analysis for Cancer Care Engineering

13 Feb. 2009 | Notes | Contributor(s): Daniel Raftery, Ann Christine Catlin

This document describes the preparation of serum samples in the Raftery Laboratory for metabolomics GCxCG-MS analysis using the LECO GC-TOF mass spectrometer.Serum samples are processed from patient whole blood at the IUSCC clinic immediately after sample acquisition, and then transferred to the …

Klaunig Oxidative Stress Analysis Laboratory

07 Feb. 2009 | Series | Contributor(s): James E. Klaunig, Ph.D., Xinzhu Pu

Studies in the laboratory of James Klaunig concentrate on understanding the mechanism by which chemicals induce cancer and the means to prevent or retard this process. Recent investigations have revolved around the role of oxidative stress and oxidative damage in the induction of cancer by …