PMID- 29605850
OWN - NLM
STAT- MEDLINE
DCOM- 20190514
LR  - 20210816
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 1766
DP  - 2018
TI  - The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas 
      Epigenomics Data.
PG  - 123-135
LID - 10.1007/978-1-4939-7768-0_7 [doi]
AB  - The Cancer Genome Atlas (TCGA) epigenome data includes the DNA methylation status 
      of tumor and normal tissues of large cohorts for dozens of cancer types. Due to 
      the moderately large data sizes, retrieving and analyzing them requires basic 
      programming skills. Simple data browsing (e.g., candidate gene search) is 
      hampered by the scarcity of easy-to-use data browsers addressed to the broad 
      community of biomedical researchers. We propose a new visualization method 
      depicting the overall DNA methylation status at each TCGA cohort while 
      emphasizing its heterogeneity, thus facilitating the evaluation of the cohort 
      variability and the normal versus tumor differences. Implemented as a trackhub 
      integrated to the University of California Santa Cruz (UCSC) genome browser, it 
      can be easily added to any genome-wide annotation layer.To exemplify the trackhub 
      usage we evaluate local DNA methylation boundaries, the aberrant DNA methylation 
      of a CpG island located at the estrogen receptor 1 (ESR1) in breast and colon 
      cancer, and the hypermethylation of the Homeobox HOXA gene cluster and the EN1 
      gene in multiple cancer types. The DNA methylation pancancer trackhub is freely 
      available at http://maplab.cat/tcga_450k_trackhub .
FAU - Mallona, Izaskun
AU  - Mallona I
AD  - Predictive and Personalized Medicine of Cancer Program, Health Research Institute 
      Germans Trias i Pujol (IGTP), Can Ruti Campus, Badalona, Spain. 
      imallona@igtp.cat.
FAU - Sierco, Alberto
AU  - Sierco A
AD  - Predictive and Personalized Medicine of Cancer Program, Health Research Institute 
      Germans Trias i Pujol (IGTP), Can Ruti Campus, Badalona, Spain.
FAU - Peinado, Miguel A
AU  - Peinado MA
AD  - IGTP, IMPPC, Badalona, Barcelona, Spain.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (EN1 protein, human)
RN  - 0 (ESR1 protein, human)
RN  - 0 (Estrogen Receptor alpha)
RN  - 0 (Homeodomain Proteins)
RN  - 157907-48-7 (HoxA protein)
SB  - IM
MH  - Atlases as Topic
MH  - Breast Neoplasms/*genetics
MH  - Colonic Neoplasms/*genetics
MH  - CpG Islands/genetics
MH  - *DNA Methylation
MH  - Data Visualization
MH  - *Epigenesis, Genetic
MH  - Estrogen Receptor alpha/genetics
MH  - Female
MH  - Genetic Association Studies
MH  - Genetic Heterogeneity
MH  - Genome, Human/*genetics
MH  - Homeodomain Proteins/genetics
MH  - Humans
MH  - Multigene Family
OTO - NOTNLM
OT  - DNA methylation
OT  - Data visualization
OT  - Pancancer
OT  - TCGA
OT  - The Cancer Genome Atlas
EDAT- 2018/04/02 06:00
MHDA- 2019/05/15 06:00
CRDT- 2018/04/02 06:00
PHST- 2018/04/02 06:00 [entrez]
PHST- 2018/04/02 06:00 [pubmed]
PHST- 2019/05/15 06:00 [medline]
AID - 10.1007/978-1-4939-7768-0_7 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2018;1766:123-135. doi: 10.1007/978-1-4939-7768-0_7.