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Genome-wide analysis of mammalian promoter architecture and evolution
These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Expand
The Transcriptional Landscape of the Mammalian Genome
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. Expand
A promoter-level mammalian expression atlas
It is found that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. Expand
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. Expand
Complex Loci in Human and Mouse Genomes
In microarray data covering a wide range of mouse tissues, genes in cis-antisense and bidirectionally promoted arrangement showed a higher probability of being coordinately expressed than random pairs of genes, implying that the presence rather than the sequence of these transcripts is of functional importance. Expand
EGASP: the human ENCODE Genome Annotation Assessment Project
The results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence. Expand
The Effects of a New Subway Line on Housing Prices in Metropolitan Toronto
An analysis by means of using the estimation results of a modal choice model and the hedonic price regressions model is conducted in order to identify the effects of a subway line in Toronto on theExpand
Discovery of estrogen receptor α target genes and response elements in breast tumor cells
Only a small core set of human genes appear to be sufficient to induce ER effects in breast cancer cells, and that cis-regulatory regions of these core ER target genes are poorly conserved suggests that different evolutionary mechanisms are operative at transcriptional control elements than at coding regions. Expand
Genomic Anatomy of the Hippocampus
Application of unbiased statistical component analyses to genome-scale hippocampal gene expression data revealed robust septotemporal molecular heterogeneity, leading to the identification of a large cohort of genes with robust regionalized hippocampal expression. Expand
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
A nearly doubled volume of published in vivo experiments on transcription factor (TF) binding is profited from to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. Expand