Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

PubWeight™: 0.79‹?›

🔗 View Article (PMID 27833659)

Published in Epigenetics Chromatin on November 09, 2016

Authors

Suhn Kyong Rhie1, Yu Guo1, Yu Gyoung Tak1, Lijing Yao1, Hui Shen2, Gerhard A Coetzee2, Peter W Laird2, Peggy J Farnham1

Author Affiliations

1: Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA.
2: Van Andel Research Institute, Grand Rapids, MI 49503 USA.

Articles cited by this

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96

Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

The accessible chromatin landscape of the human genome. Nature (2012) 16.86

A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02

Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature (2007) 10.94

Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93

FIMO: scanning for occurrences of a given motif. Bioinformatics (2011) 8.89

A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature (2013) 5.18

The Molecular Taxonomy of Primary Prostate Cancer. Cell (2015) 3.29

Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer. Cancer Res (2007) 2.95

Genomics: ENCODE explained. Nature (2012) 2.62

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol (2012) 2.19

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility. Genome Res (2012) 1.77

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol (2013) 1.71

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res (2014) 1.63

Identification of a Candidate Gene Panel for the Early Diagnosis of Prostate Cancer. Clin Cancer Res (2015) 1.57

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep (2015) 1.54

Screening for prostate cancer. CA Cancer J Clin (2009) 1.48

Biology and clinical relevance of the micropthalmia family of transcription factors in human cancer. J Clin Oncol (2011) 1.47

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet (2014) 1.44

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods (2015) 1.27

Loss of HOXC6 expression induces apoptosis in prostate cancer cells. Oncogene (2005) 1.23

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol (2014) 1.12

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol (2015) 0.98

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genomics (2014) 0.94

Identification and characterization of renal cell carcinoma gene markers. Cancer Inform (2007) 0.92

Prostate cancer metastasis-driving genes: hurdles and potential approaches in their identification. Asian J Androl (2014) 0.84

The hypoxia-inducible transcription factor ZNF395 is controlled by IĸB kinase-signaling and activates genes involved in the innate immune response and cancer. PLoS One (2013) 0.83

The role of HOXC6 in prostate cancer development. Prostate (2015) 0.82

CaMKK2: a novel target for shaping the androgen-regulated tumor ecosystem. Trends Mol Med (2013) 0.82

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Res (2016) 0.80

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. Genome Res (2016) 0.79

The Transcription Factor ZNF395 Is Required for the Maximal Hypoxic Induction of Proinflammatory Cytokines in U87-MG Cells. Mediators Inflamm (2015) 0.78

RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma. Biomed Res Int (2014) 0.78