scholarly journals CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data

2018 ◽  
Vol 11 (S2) ◽  
Author(s):  
Seonggyun Han ◽  
Dongwook Kim ◽  
Youngjun Kim ◽  
Kanghoon Choi ◽  
Jason E. Miller ◽  
...  
Keyword(s):  
Integrative Analysis ◽  
Web Based ◽  
Cancer Data

scholarly journals Identification of Breast Cancer Prognosis Markers Using Integrative Sparse Boosting

2012 ◽  
Vol 51 (02) ◽  
pp. 152-161 ◽  
Author(s):  
J. Huang ◽  
Y. Xie ◽  
N. Yi ◽  
S. Ma
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Failure Time ◽  
Prediction Performance ◽  
Small Sample ◽  
Integrative Analysis ◽  
Breast Cancer Prognosis ◽  
Cancer Prognosis ◽  
Cancer Data ◽  
Genomic Markers

SummaryObjectives: In breast cancer research, it is important to identify genomic markers associated with prognosis. Multiple microarray gene expression profiling studies have been conducted, searching for prognosis markers. Genomic markers identified from the analysis of single datasets often suffer a lack of reproducibility because of small sample sizes. Integrative analysis of data from multiple independent studies has a larger sample size and may provide a cost-effective solution.Methods: We collect four breast cancer prognosis studies with gene expression measurements. An accelerated failure time (AFT) model with an unknown error distribution is adopted to describe survival. An integrative sparse boosting approach is employed for marker selection. The proposed model and boosting approach can effectively accommodate heterogeneity across multiple studies and identify genes with consistent effects.Results: Simulation study shows that the proposed approach outperforms alternatives including meta-analysis and intensity approaches by identifying the majority or all of the true positives, while having a low false positive rate. In the analysis of breast cancer data, 44 genes are identified as associated with prognosis. Many of the identified genes have been previously suggested as associated with tumorigenesis and cancer prognosis. The identified genes and corresponding predicted risk scores differ from those using alternative approaches. Monte Carlo-based prediction evaluation suggests that the proposed approach has the best prediction performance.Conclusions: Integrative analysis may provide an effective way of identifying breast cancer prognosis markers. Markers identified using the integrative sparse boosting analysis have sound biological implications and satisfactory prediction performance.

scholarly journals Western Honduras Copán Population–Based Cancer Registry: Initial Estimates and a Model for Rural Central America

2021 ◽  
pp. 1694-1702
Author(s):  
Dalton Argean Norwood ◽  
Eleazar Enrique Montalvan-Sanchez ◽  
Juan E. Corral ◽  
Dagoberto Estévez-Ordoñez ◽  
Andrea A. Paredes ◽  
...  
Keyword(s):  
Central America ◽  
Cancer Control ◽  
Cancer Registries ◽  
Population Based ◽  
Incidence Rates ◽  
Western Hemisphere ◽  
Ancillary Data ◽  
Web Based ◽  
Cancer Data ◽  
Males And Females

PURPOSE Population-based cancer registries (PBCRs) are critical for national cancer control planning, yet few low- and middle-income countries (LMICs) have quality PBCRs. The Central America Four region represents the principal LMIC region in the Western hemisphere. We describe the establishment of a PBCR in rural Western Honduras with first estimates for the 2013-2017 period. METHODS The Western Honduras PBCR was established through a collaboration of academic institutions and the Honduras Ministry of Health for collection of incident cancer data from public and private health services. Data were recorded using the Research Electronic Data Capture (REDCap) web-based platform with data monitoring and quality checks. Crude and age-standardized rates (ASRs) were calculated at the regional level, following WHO methodology. RESULTS The web-based platform for data collection, available ancillary data services (eg, endoscopy), and technical support from international centers (United States and Colombia) were instrumental for quality control. Crude cancer incidence rates were 112.2, 69.8, and 154.6 per 100,000 habitants overall, males, and females, respectively (excluding nonmelanoma skin cancer). The adjusted ASRs were 84.2, 49.6, and 118.9 per 100,000 overall habitants, males, and females, respectively. The most common sites among men were stomach (ASR 26.0, 52.4%), colorectal (ASR 5.11, 10.15%), and prostate (ASR 2.7, 5.4%). The most common sites in women were cervix (ASR 34.2, 36.7%), breast (ASR 11.2, 12.3%), and stomach (ASR 10.8, 11.7%). CONCLUSION The Copán-PBCR represents a successful model to develop cancer monitoring in rural LMICs. Innovations included the use of the REDCap platform and leverage of Health Ministry resources. This provides the first PBCR data for Honduras and the Central America Four and confirms that infection-driven cancers, such as gastric and cervical, should be priority targets for cancer control initiatives.

scholarly journals Omics Fusion – A Platform for Integrative Analysis of Omics Data

2016 ◽  
Vol 13 (4) ◽  
pp. 43-46 ◽  
Author(s):  
Benedikt G. Brink ◽  
Annica Seidel ◽  
Nils Kleinbölting ◽  
Tim W. Nattkemper ◽  
Stefan P. Albaum
Keyword(s):  
Integrative Analysis ◽  
Omics Data ◽  
Web Based

Summary We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/

scholarly journals Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

Oncogenesis ◽  
2015 ◽  
Vol 4 (7) ◽  
pp. e160-e160 ◽  
Author(s):  
I Kuperstein ◽  
E Bonnet ◽  
H-A Nguyen ◽  
D Cohen ◽  
E Viara ◽  
...  
Keyword(s):  
Systems Biology ◽  
Integrative Analysis ◽  
Google Maps ◽  
Cancer Data ◽  
Signalling Network

scholarly journals Role of Theories in the Design of Web-Based Person-Centered Support: A Critical Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-9
Author(s):  
Agneta Ranerup ◽  
Carina Sparud-Lundin ◽  
Ingalill Koinberg ◽  
Ingela Skärsäter ◽  
Margaretha Jenholt-Nolbris ◽  
...  
Keyword(s):  
Participatory Design ◽  
Well Being ◽  
Web Based ◽  
Cancer Data ◽  
Early Motherhood ◽  
Design Learning ◽  
Person Centered Approach ◽  
Health And Well Being

Objective. The aim of this study was to provide a critical understanding of the role of theories and their compatibility with a person-centered approach in the design and evaluation of web-based support for the management of chronic illness.Methods. Exploration of web-based support research projects focusing on four cases: (1) preschool children aged 4–6 with bladder dysfunction and urogenital malformation; (2) young adults aged 16–25 living with mental illness; (3) women with type 1 diabetes who are pregnant or in early motherhood; and (4) women who have undergone surgery for breast cancer. Data comprised interviews with research leaders and documented plans. Analysis was performed by means of a cross-case methodology.Results. The used theories concerned design, learning, health and well-being, or transition. All web support products had been developed using a participatory design (PD). Fundamental to the technology design and evaluation of outcomes were theories focusing on learning and on health and well-being. All theories were compatible with a person-centered approach. However, a notable exception was the relatively collective character of PD and Communities of Practice.Conclusion. Our results illustrate multifaceted ways for theories to be used in the design and evaluation of web-based support.

The PBL-Evaluator: a web-based tool for assessment in tutorials

1998 ◽  
Vol 62 (9) ◽  
pp. 671-674
Author(s):  
JF Chaves ◽  
JA Chaves ◽  
MS Lantz
Keyword(s):  
Web Based
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