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University of Texas MD Anderson Cancer Center
Statistical Issues in Proteomic Research
Jeffrey S. Morris Thu, 31 Jul 2008 11:03:24 -0700
Microproteomics: Analysis of protein diversity in small samples
Howard B. Gutstein Fri, 13 Jun 2008 14:38:53 -0700
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Jeffrey S. Morris Tue, 04 Dec 2007 09:44:53 -0800
Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust, and reproducible methods for detecting, matching, and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels, and finally quantifying each spot by calculating normalized spot volumes. This approach is time con-suming, error-prone, and frequently requires extensive manual edit-ing, which can unintentionally introduce bias into the results.Results: We introduce a new method for spot detection and quanti-fication called Pinnacle that is automatic, quick, sensitive and spe-cific, and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller CVs. More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.
Laser capture sampling and analytical issues in proteomics
Howard Gutstein Tue, 04 Dec 2007 09:35:54 -0800
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
Statistical contributions to proteomic research
Jeffrey S. Morris Wed, 04 Apr 2007 12:55:09 -0700
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the key statistical principles that should guide the experimental design and analysis of such studies.
Wavelet-based functional mixed model analysis: Computational considerations
Richard C. Herrick Wed, 04 Apr 2007 12:48:45 -0700
Wavelet-based Functional Mixed Models is a new Bayesian method extending mixed models to irregular functional data (Morris and Carroll, JRSS-B, 2006). These data sets are typically very large and can quickly run into memory and time constraints unless these issues are carefully dealt with in the software. We reduce runtime by 1.) identifying and optimizing hotspots, 2.) using wavelet compression to do less computation with minimal impact on results, and 3.) dividing the code into multiple executables to be run in parallel using a grid computing resource. We discuss rules of thumb for estimating memory requirements and computation times in terms of model and data set parameters. We present examples and benchmarks demonstrating that it is practical to analyze very large data sets with readily available computing resources. This code is freely available on our website.
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Statistical Issues in Proteomic Research
Jeffrey S. Morris Thu, 31 Jul 2008 11:03:24 -0700
Microproteomics: Analysis of protein diversity in small samples
Howard B. Gutstein Fri, 13 Jun 2008 14:38:53 -0700
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
Pinnacle: A Fast, Automatic Method for Detecting and Quantifying Protein Spots in 2-Dimensional Gel Electrophoresis Data
Jeffrey S. Morris Tue, 04 Dec 2007 09:44:53 -0800
Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust, and reproducible methods for detecting, matching, and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels, and finally quantifying each spot by calculating normalized spot volumes. This approach is time con-suming, error-prone, and frequently requires extensive manual edit-ing, which can unintentionally introduce bias into the results.Results: We introduce a new method for spot detection and quanti-fication called Pinnacle that is automatic, quick, sensitive and spe-cific, and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller CVs. More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.
Laser capture sampling and analytical issues in proteomics
Howard Gutstein Tue, 04 Dec 2007 09:35:54 -0800
Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for the analysis of the highly complex datasets generated are also reviewed.
Statistical contributions to proteomic research
Jeffrey S. Morris Wed, 04 Apr 2007 12:55:09 -0700
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the key statistical principles that should guide the experimental design and analysis of such studies.
Wavelet-based functional mixed model analysis: Computational considerations
Richard C. Herrick Wed, 04 Apr 2007 12:48:45 -0700
Wavelet-based Functional Mixed Models is a new Bayesian method extending mixed models to irregular functional data (Morris and Carroll, JRSS-B, 2006). These data sets are typically very large and can quickly run into memory and time constraints unless these issues are carefully dealt with in the software. We reduce runtime by 1.) identifying and optimizing hotspots, 2.) using wavelet compression to do less computation with minimal impact on results, and 3.) dividing the code into multiple executables to be run in parallel using a grid computing resource. We discuss rules of thumb for estimating memory requirements and computation times in terms of model and data set parameters. We present examples and benchmarks demonstrating that it is practical to analyze very large data sets with readily available computing resources. This code is freely available on our website.
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Cancer.gov: Information from the National Cancer Institute about cancer treatment, prevention, screening, genetics, causes, and how to cope with cancer.CancerGuide: Provides a comprehensive orientation to help motivated patients begin to actively engage their disease and their health care team.
Acronyms: Cancer dictionary - words, phrases, acronyms, and terminology in a searchable glossary styled format.
Cancer Foundation: AOL discussion group aimed at providing information and support.
Issues: Hematology and Oncology News & Issues, If legislators dont have to live with Medicare, should they be directing its future?
Pediatric Cancers: Comprehensive information and support for Rare Adult Cancer patients and Pediatric Cancer patients.
A: About AllExperts: expert guidance from real people helping to answer your questions
About.com Cancer: Latest articles from the Cancer GuideSite.
About.com: Cancer: In this cancer resource, you will find information about symptoms of several types of cancer, cancer causes, treatment and more. Cancer Prevention and risk factors such as HPV, smoking, and other carconigens are discussed as well.
ACOR Support: Links-based listing by the Association of Online Cancer Resources.
ACS: Statistics: The American Cancer Society tracks cancer occurence, including the number of deaths, cases, and how long people survive after diagnosis. ACS also tracks data regarding behaviors that influence the risk of developing cancer and the use of screening tests.
atCancer: Gives access to a MEDLINE-related search engine, as well as to reference links.
BBC News: Cancer the Facts: A guide to several types of tumors and their treatments including audio from experts, survivors' stories and news archives.
Beat Cancer Page: Get some pixels and link your website
Cancer Advice UK: Advice and information on cancers such as breast cancer, bladder cancer, brain tumours, cervical cancer, cancer of the colon, Hodgkin's Disease, lung cancer, melanoma, ovarian cancer, prostate cancer, testicular cancer, uterine cancer
Cancer Chart: Quick reference listing of the most common tumor types.
Cancer Consultants.com: Provides information on treatment and prevention for patients and professionals.
Cancer Forums: Online discussions on various types of tumors. Includes topics such as coping, support, clinical trials and treatment options.
Cancer Information Services: The Cancer Information Service (CIS) is your source for the latest, most accurate cancer information from the National Cancer Institute (NCI).
Cancer Innovations: Articles and webcasts on different types of cancer including; lung cancer, colon cancer, colorectal cancer and more. Cancer information cancer symptoms, medication and therapy.
Cancer Leadership Council: A patient-centered forum of national advocacy organizations addressing public policy issues.
Cancer Lynx: Cancer Lynx - We Prowl the Net Advocating for cancer patients and their families. Your source for news information and very human stories about cancer
Cancer Matters: Designed to help you find the resources you need, the Cancer Matters Resource Guide offers a list of services, products and providers that specifically meet the needs of those with cancer, as well as those of their caregivers, family and friends.
Cancer Mondial: The International Agency for Research on Cancer provides access to reports and databases on occurrence and characteristics.
Cancer Monthly: Cancer Monthly provides information about 100s of cancer treatments so that patients can compare therapy differences, longest survival rates, toxicity, side effects, hospitals, and many other facts, to have more meaningful discussions with their doctors, and ultimately, make more informed treatme...
Cancer Network.com: Leading oncologists offer research and opinion on the screening, early detection, diagnosis, treatment, and prevention cancers.
Cancer Nutrition Center: Explores the link between tumors and nutrition. Offers dietary advice for patients.
Cancer Options UK: Cancer Options is a service designed to help people with cancer and their families find the treatment options and services they need
Cancer Page: CancerPage,cancer information and community resource.
Cancer Rates and Risks: Provides international incidence and mortality rates including information about risk factors. From the U.S. National Cancer Institute.
Cancer Resource UK: Easyspace offers domain ownership from just $5 per year. Free and low cost web hosting packages. Over 500,000 clients world-wide MySQL database support, Real Audio and Video streaming. Great domain and hosting reseller packages
Cancer Site Finder.com: CancerSiteFinder.com: Your Guide to Cancer Websites [SiteFinders > CancerSiteFinder.com]| Choose a CancerTopicBladderBlood (Leukemia)Blood (Multiple Myeloma)BoneBrainBreastCervicalColonGeneral Cancer SitesHead and NeckKidneyLiverLungLymphomaOvarianPancreaticProstateSkinStomach (Gastric)Testic...
Cancer Story: Cancer Story: A Public Television Program
Cancer Support Links: This webiste contains online support and information resources for a variety of cancers. These resources include information about the disease, treatment options, clinical trial searches, online message boards, chat rooms, email list groups/ListServs and more.
Cancer Surveillance On-Line: The following pages of this website will provide you with the most current cancer statistics in Canada. You will be able to look at trends in cancer incidence by province and territory, by age group, over time, and for about 45 different cancer sites. Both graphs and tables will be displayed and ...
Cancer Survivors Project: The Cancer Survivors Project is an organized, international community of long-term cancer survivors and their friends working together to improve the lives of children and adults after cancer. CSP is committed to making available information regarding physiological and psychosocial late effe...
Cancer.com: The leading portal for links to cancer information, cancer prevention news and cancer treatment options.
Cancer/Oncology News From Medical News Today: Press releases and news articles about research findings and treatments.
CancerBACUP: Cancerbackup - Europe's leading cancer information service, providing accurate, up-to-date and authorative cancer information, resources and support for people affected by cancer.
CancerDirect: cancer patient consultation service offering case review, cancer treatment advice, online second opinions and oncologist referral for individual diseases
CancerEducation: Disseminates educational programming in a multimedia electronic clips format. Aimed at both a lay and professional audience.
CancerExperts MD: Cancer Experts. Providers of second opinions and personalized cancer case reviews. Medical reviews for cancer patients in need of alternative personalized case anaylyses.
CancerFit: CancerFit is an exercise program designed to help people tolerate cancer treatment and regain physical fitness after treatment.
CancerHelpOnline: Cancer information. Cancer may be preventable. Latest medical reasearch showes antioxidants help.
CancerLinks.org: Cancer A to Z Links - A thoughtful source and guide to cancer information on the World Wide Web. Choose from hundreds of helpful and useful links world wide with more added daily for your cancer needs.
CancerNausea.com: CancerNausea.com is a website for people experiencing nausea and vomiting caused by chemotherapy or radiation treatments. Our goal is to provide clear, useful information that will help you gain more control over your health and well-being.Upcoming Event. Oncology Nursing Society. MASCC - Geneva ...
CancerNews.com: Cancer News on the Net® is dedicated to bringing patients and their families the latest information on cancer diagnosis, treatment andprevention. We are constantly searching for the best cancer information sources that are available on the Net.
CancerSource: Provides information about prevention, detection, diagnosis, treatment and symptom management. Offers access to news, support groups and email lists.
CancerSupport UK: An on-line directory of resources for anyone affected by cancer in the UK
CancerSymptoms: Discusses common symptoms related to cancer treatment. Provides email access to a nurse for questions.
CancerTrack: Tracking cancer information online. Cancer News, Books and Links. Up to date information on cancer. News updated every 15 minutes, Books and thousands of cancer web sites. Searches provide detailed current information on requests.
Cellscience: A-Z Cancer Directory: International A-Z medical information directory covering Cancer research, hospitals, clinics, charities and information resources
Chemo Care: Welcome to Chemocare.com, my (Scott Hamilton) new website designed to provide the latest information about chemotherapy to patients and their families, caregivers and friends. Cancer is a complicated, challenging disease. We're here to help alleviate you concerns by outlining everything you nee...
Chemotherapy and Beyond: Welcome to Chemocare.com, my (Scott Hamilton) new website designed to provide the latest information about chemotherapy to patients and their families, caregivers and friends. Cancer is a complicated, challenging disease. We're here to help alleviate you concerns by outlining everything you nee...
Chemotherapy.com: Provides educational information on therapy for cancer patients, including chemo side-effects. Sponsored by the Amgen firm.
Conversations in Care: Talking about care can be a challenge for both healthcare professionals and patients, particularly in the field of oncology. Conversations in Care is dedicated to improving healthcare through better physician/patient communications.
DIPEx: Cancer: Patient Experieces of health and illness is a resource, which aims to show what the experience of illness is really like for patients, their carers and families.
Don't Say That Word: Provides an online forum on cancer, information, personal stories, poetry and remembrance pages. Graphics-intensive.
eMedicine Health: What You Need to Know: The news comes like a sledgehammer into the stomach:
eMedicine Health: Cancer Symptoms: Cancer often has no specific symptoms, so it is important that you limit your risk factors and undergo appropriate cancer screening.Nevertheless, you need to know which symptoms might point to ...
Guide to Internet Resources for Cancer: Non-profit directory of information sorted by disease type, country and treatment.
HCA Cancer Guides: This is the Home Page for the Website.
Imperial Cancer Research Fund: Cancer Research UK, the UK's leading cancer charity. This site has a wealth of information about the charity and about cancer. We also have many ways for you to make a donation or to support our vital cancer research.
Ladies Home Journal: Cancer: Cancer Information from Ladies' Home Journal
Lymphomaniacs: Lymphomaniacs.org
Manage CINV: ManageCINV.com is a resource dedicated to providing up-to-date information about chemotherapy-induced nausea and vomiting (CINV). The content on ManageCINV.com is tailored to meet the specific needs of Patients, Physicians, Nurses and Pharmacists.
MCW: Cancer Information: MCW HealthLink articles on Cancer
MedicineNet: Cancer: Information on many different cancers includes symptoms, cancer detection and prevention, and treatment options.
Meds.com: Cancer Glossary: Glossary of Cancer terms Answers to all your questions like what is leukemia, what is hepatitis B or what is hepatitis C, mesothelioma, chemotherapy and more such definitions and explanations of cancer related terms. Find answers to common questions like what is chemotherapy, what is hepatiti...
Mount Zion: Hyperthermia Treatment: Website to promote the Hyperthermia clinic at UCSF
Multinational Association of Supportive Care in Cancer: The Multinational Association of Supportive Care in Cancer is an international, multidisciplinary organization with over 1000 members representing more than thirty countries and five continents. It operates in collaboration with the International Society for Oral Oncology. Founded in 1990, this ...
National Comprehensive Cancer Network: The National Comprehensive Cancer Network (NCCN), an alliance of 21 of the world's leading cancer centers, is an authoritative source of comprehensive cancer care information that strives to insure the quality of cancer care and advance clinical research. Through the collaborative expertise of it...
Nature: Cancer Update: Nature - the world's best science and medicine on your desktop
NCCN and ACS: Cancer Treatment Options: Guidelines by the American Cancer Society and the National Comprehensive Cancer Network on early detection, staging, support, care and treatment side-effects for a number of tumors.
NCI Center for Cancer Research: U.S. government resource which provides access to information for researchers and about collaborations. Aimed at the professional level.
NCI: Dictionary of Cancer Terms: Glossary offered by the U.S. National Cancer Institute.
NetCancerAlert: This website offers links cancer resources and up to the date cancer therapy, doctor, reviews, and second opinions
Nexcura: Cancer Facts: NexCura provides dynamic, evidence-based applications that allow patients and their physicians to gather precise, relevant medical information about cancer research treatment options, side-effects, life-expectancy and outcomes.
On Top of Cancer: Cancer information, treatment, support guide by doctor, survivor group.
OncoLink: OncoLink, the Web's first cancer resource, provides comprehensive information on cancer treatments, cancer research advances, continuing medical education, cancer prevention, and clinical trials.
Oncology Interactive Education Series: Commercial audio-visual educational resources for patients.
People Living with Cancer: People Living With Cancer (www.plwc.org) - accurate, reliable and oncologist approved cancer information from the world's leading organization representing medical professionals who treat people with cancer.
Radiofrequency Ablation: Cancer: Brief summary of a technique which may be used for treatment. Includes a FAQ, message board and illustrations.
Rare Tumors.org: Web-based resource that presents information on a number of the less common cancers.
Suite 101: The articles on the topic of new cancer treatments are based on a greatly improved understanding of the nature of cancers.This understanding of how cancer cells differ from normal cells has allowed the researcher to develop very specific and effective treatments. Current treatments, namely surge...
Target Tumors: Target Tumors - Cancer and tumor articles and webcasts about brain tumors, lung cancer and prostate cancer. Research on prostate cancer, gist treatments and gleevec.
Telematics Services in Cancer: TeleSCAN offers access to resources aimed for European oncologists. Provides links, general information and an intra-site search tool for specific diseases.
The Cancer Information Network: Global cancer information providor
The Cancer Letter: News and information about cancer research funding and policy.
The Cancer Supportive Care Programs: Cancer Supportive Care is the Fifth Dimension Therapy of cancer care providing educational modules to complement surgery, radiation, chemotherapy, hormonal therapy and immunotherapy
The World Against Cancer: multiple multi featured multilingual search one-stop cancer information source web site
Tirgan: Chemotherapy Drugs: Information on about thirty commonly employed drug-agents used in the treatment of cancer.
Untangling the Web: Links to disability Web sites
USnews.com: Best Cancer Hospitals: Get health information, including our annual list of the best hospitals in America, for yourself and your family.
WebMD Health: Cancer: Start here for information on common types of cancer, including breast, lung, colon, skin, prostate, and ovarian cancer. Get the facts on cancer symptoms, treatments, and recovery.
Wikicities: Cancer: An open-publishing wiki portal for those interested in this topic. Available for viewing or editing.
World Oncology Network: World Oncology Network (WON) is a worldwide network of physicians and nurses practicing Hematology and Oncology.Also provides public and patient information about most cancers and their treatments
Yahoo Health: Cancer and Chemotherapy: Information in links and article form including basic facts, what to expect and side effects.
This directory is based on the Open Directory and may have been modified