Repositorio
Institucional

Huang, Tim H. M.

Gu, Fei

Doderer, Mark S.

Huang, Yi-Wen

Roa, Juan C.

Goodfellow, Paul J.

Kizer, E. Lynette

Chen, Yidong

CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers

PUBLIC LIBRARY SCIENCE

PLOS ONE

en

Background: DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters. Methodology/Principal Findings: Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework. Conclusions/Significance: CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible at: http://cbbiweb.uthscsa.edu/KMethylomes/.

Artículo original

This work was supported by R01 CA069065, U54 CA113001 (Integrative Cancer Biology Program), P30 CA054174 (Cancer Center Support Grant), NCATS 8UL1TR000149 (CTSA) of the U.S. National Institutes of Health, Texas CPRIT RP101195-C04, and by generous gifts from the Cancer Therapy and Research Center Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Este trabajo fue financiado por las subvenciones R01 CA069065, U54 CA113001 (Programa Integrativo de Biología del Cáncer), P30 CA054174 (Subvención de Apoyo al Centro Oncológico), NCATS 8UL1TR000149 (CTSA) de los Institutos Nacionales de Salud de EE. UU., Texas CPRIT RP101195-C04 y por generosas donaciones de la Fundación del Centro de Investigación y Terapia del Cáncer. Los financiadores no participaron en el diseño del estudio, la recopilación y el análisis de datos, la decisión de publicar ni la preparación del manuscrito.

10.1371/journal.pone.0060980

pdf

DNA METHYLATION

BREAST-CANCER

GENE-EXPRESSION

HIGH-THROUGHPUT

CELLS

HOXB2

METHYLOME

PATTERNS

GROWTH

METILACIÓN DEL ADN

CÁNCER DE MAMA

EXPRESIÓN GÉNICA

ALTO RENDIMIENTO

CÉLULAS

HOXB2

METILOMA

PATRONES

CRECIMIENTO

DNA METHYLATION

BREAST-CANCER

GENE-EXPRESSION

HIGH-THROUGHPUT

CELLS

HOXB2

METHYLOME

PATTERNS

GROWTH

METILACIÓN DEL ADN

CÁNCER DE MAMA

EXPRESIÓN GÉNICA

ALTO RENDIMIENTO

CÉLULAS

HOXB2

METILOMA

PATRONES

CRECIMIENTO

Ciencias de la Información y Bioinformática

Oncología

Tecnología para la Identificación y Funcionamiento del ADN, Proteínas y Encimas y como influyen en la aparición de enfermedades y la mantención del bienestar (Diagnóstico e intervenciones terapéuticas basados en genes (Farmacogenómica, terpaias basadas en genes)

CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers

PLOS ONE

dorada

verde

acceso abierto

acceso abierto

PMID 23630576

en

Artículo original

versión publicada

NIH Integrative Cancer Biology Program R01 CA069065#NIH Integrative Cancer Biology Program U54 CA113001#NIH Cancer Center Support Grant P30 CA054174#U.S. National Institutes of Health, Texas NCATS 8UL1TR000149 (CTSA)#NIH CPRIT RP101195-C04#NIH, National Cancer Institute P30CA054174

NIH Integrative Cancer Biology Program R01 CA069065

NIH Integrative Cancer Biology Program U54 CA113001

NIH Cancer Center Support Grant P30 CA054174

U.S. National Institutes of Health, Texas NCATS 8UL1TR000149 (CTSA)

NIH CPRIT RP101195-C04

NIH, National Cancer Institute P30CA054174

PUBLIC LIBRARY SCIENCE

1932-6203

e60980

Ciencias multidisciplinarias

Multidisciplinary Sciences

pdf

WOS:000317911500011