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WebLogo: a sequence logo generator.
WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarityExpand
Human DNA methylomes at base resolution show widespread epigenomic differences
The first genome-wide, single-base-resolution maps of methylated cytosine methylation in a mammalian genome are presented, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA–protein interaction for several key regulatory factors. Expand
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Insight is given into the connections between chromatin modifications and transcriptional regulatory activity and a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2) is uncovered, providing a new tool for the functional annotation of the human genome. Expand
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts. Expand
Histone modifications at human enhancers reflect global cell-type-specific gene expression
The results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression. Expand
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
The first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells are reported. Expand
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
Application of Tet-assisted bisulfite sequencing to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at5hmC sites. Expand
The ASTRAL Compendium in 2004
The ASTRAL Compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences, and all SCOP domains are now made available as PDB-style coordinate files as well as sequences. Expand
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
By comparing the chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, it is found that nearly one-third of the genome differs in chromatin structure. Expand
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
The results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells. Expand