Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

CS Ross-Innes, R Stark, AE Teschendorff, KA Holmes… - Nature, 2012 - nature.com
Oestrogen receptor-α (ER) is the defining and driving transcription factor in the majority of
breast cancers and its target genes dictate cell growth and endocrine response, yet genomic …

The MEME suite

TL Bailey, J Johnson, CE Grant… - Nucleic acids …, 2015 - academic.oup.com
The MEME Suite is a powerful, integrated set of web-based tools for studying sequence
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …

Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor

JM Gendron, JL Pruneda-Paz… - Proceedings of the …, 2012 - National Acad Sciences
The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal
regulation between TIMING OF CAB EXPRESSION 1 (TOC1) and CIRCADIAN CLOCK …

Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis

X Xia, ME Lemieux, W Li, JS Carroll… - Proceedings of the …, 2009 - National Acad Sciences
Adaptation to hypoxia is mediated through a coordinated transcriptional response driven
largely by hypoxia-inducible factor 1 (HIF-1). We used ChIP-chip and gene expression …

Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1

JLL Robinson, S MacArthur, CS Ross‐Innes… - The EMBO …, 2011 - embopress.org
Breast cancer is a heterogeneous disease and several distinct subtypes exist based on
differential gene expression patterns. Molecular apocrine tumours were recently identified …

Direct regulation of abiotic responses by the A rabidopsis circadian clock component PRR 7

T Liu, J Carlsson, T Takeuchi, L Newton… - The plant …, 2013 - Wiley Online Library
Up to 30% of the plant transcriptome is circadian clock‐regulated in different species;
however, we still lack a good understanding of the mechanisms involved in these genome …

Comparative analysis of regulatory information and circuits across distant species

AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng… - Nature, 2014 - nature.com
Despite the large evolutionary distances between metazoan species, they can show
remarkable commonalities in their biology, and this has helped to establish fly and worm as …

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

CL Plaisier, M Pan, NS Baliga - Genome research, 2012 - genome.cshlp.org
Genes regulated by the same miRNA can be discovered by virtue of their coexpression at
the transcriptional level and the presence of a conserved miRNA-binding site in their 3 …

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

PM Fordyce, D Gerber, D Tran, J Zheng, H Li… - Nature …, 2010 - nature.com
Gene expression is regulated in part by protein transcription factors that bind target
regulatory DNA sequences. Predicting DNA binding sites and affinities from transcription …

Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

H Wang, J Jiang, S Chen, X Qi, H Peng, P Li, A Song… - PloS one, 2013 - journals.plos.org
Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes.
Chrysanthemum is one of the largest genera in the Asteraceae family. Only few …