Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

By M. Berger, Gwenael Badis, Andrew R. Gehrke, Shaheynoor Talukder, A. Philippakis, Lourdes Peña-Castillo, Trevis M. Alleyne, S. Mnaimneh, O. Botvinnik, Esther T. Chan and 7 more. Cell, 2008

670 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/30deb60b49de20dfa2525c9160d1884ded2c2af1

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Citations in the corpus

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010) (2010, positive): “ChIP and PBMs have been applied to map transcriptional networks in a variety of human cell types, including stem cells (Cole et al., 2008; Lee et al., 2006) and lymphocytes (Marson et al., 2007; Schreiber et al., 2006), and to characterize the binding motifs of many mammalian TF families (Berger et ”
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions (2014, methodology): “Publications with data in UniPROBE whose protein pages currently link to TFBSshape (and vice versa) are: Berger et al. , 2006 (1); Berger et al. , 2008 (26); Zhu et al. , 2009 (27); Badis et al. , 2009 (28); Lesch et al. , 2009 (30); Scharer et al. , 2009 (32).”
Annotation of functional variation in personal genomes using RegulomeDB (2012, methodology): “Secondly, we scanned the genome at a reasonable threshold for added positional weight matrices (PWMs) (Berger et al. 2006, 2008; Matys et al. 2006; Bryne et al. 2008; Badis et al. 2009; Scharer et al. 2009; Wei et al. 2010), which were further used to intersect with other functional data (see…”
An atlas of combinatorial transcriptional regulation in mouse and man (2010, positive): “…have been applied to map transcriptional networks in a variety of human cell types, including stem cells (Cole et al., 2008; Lee et al., 2006) and lymphocytes (Marson et al., 2007; Schreiber et al., 2006), and to characterize the binding motifs of many mammalian TF families (Berger et al., 2008).”
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data (2014, methodology): “In an additional test on two other PBM data sets covering 115 human and mouse E26 transformation-specific (ETS) and homeodomain TFs tested on a single array (19,20), HT-SELEX-derived models achieved an average AUC of 0.”
Densely interconnected transcriptional circuits control cell states in human hematopoiesis (2011, positive): “The 396 enriched motifs were compared to a library of previously published motifs of known transcription factors (Badis et al., 2009; Berger et al., 2008; Chang et al., 2008; Matys et al., 2003; Sandelin et al., 2004).”
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles (2009, background): “PBM_HOMEO, the set derived by (40) includes 176 profiles from mouse homeodomains.”
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo (2013, methodology): “We adapted protein binding DNA microarray technology (Berger and Bulyk 2006; Berger et al. 2006, 2008) to evaluate how CG methylation affects binding of eight B-ZIP homodimers and the CEBPB|ATF4 heterodimer.”
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. (2010, background): “In cases where the existing profiles were derived from more sequences or were generated using protein-binding microarrays (Berger et al. 2008; Badis et al. 2009), our profiles were in good agreement with the existing data.”
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo (2010, positive): “Similarly, individually analysed homeobox-TF-binding profiles were found to be more divergent compared with those reported in two syste- matic studies (Berger et al, 2008; Noyes et al, 2008).”
UniPROBE: an online database of protein binding microarray data on protein–DNA interactions (2008, neutral): “The site currently hosts PBM data for over 175 nonredundant proteins from a wide range of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenor”
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution (2015, background): “Within each TF family, DNA binding specificity has also diverged considerably, with many families having 2–10 different subclasses displaying different primary binding specificities (Berger et al., 2008; Wei et al., 2010; Jolma et al., 2013).”
Homeodomain proteins: an update (2015, background): “This resulted in databases where binding site preferences for individual transcription factors, or their DNA-binding domain, can be looked up (Affolter et al. 2008; Berger et al. 2008; Jolma et al. 2013; Noyes et al. 2008), for example, in Jaspar (http:// jaspar.genereg.net) (Mathelier et al. 2014).”