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Examples include GBIF for primary data, Encyclopedia of Life (EOL) [ 89] for species descriptions, uBio [ 90] and Global Names Index [ 38] for names usages, CoL [ 40] for validated species names and Europeana [ 91] for multimedia resources.
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Significant DEGs were categorized based on cellular function according to GO (Gene Ontology) and KEGG data (Kyoto Encyclopedia of Genes and Genomes).
Data from Encyclopedia of DNA elements project showed that these regions are DNase I hypersensitive and able to bind various transcription factors, which suggests a promoter or enhancer activity [ 22].
Using TF targeted chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) data from Encyclopedia of DNA Elements (ENCODE), we report cell type and TF specific TF-cofactor interactions captured in vivo through enrichments of non target cofactor binding site motifs within ChIP-seq peaks.
The National Human Genome Research Institute NHGRII) established a 9-month moratorium on publication by third parties of data from the Encyclopedia of DNA Elements (ENCODE).
In our study we used human ChIP-seq data from The Encyclopedia of DNA Elements (ENCODE) Project [ 17].
We collected high-throughput sequencing data from the ENCyclopedia Of DNA Elements (ENCODE), the Gene Expression Omnibus (GEO) and the European Nucleotide Archive ENAA).
Gene Ontology Biological Process and KEGG pathways data bases (Kyoto Encyclopedia of Genes and Genomes, Kanehisa, Goto et al., 2002) were considered.
Data from the Encyclopedia of DNA elements project showed that the analyzed CpG rich region upstream of HSD17B1 (chr17: 37 953 426-37 954 646) is able to bind various transcription factors.
The regions for analysis were chosen using findings from the literature and bioinformatics, especially epigenetic data from the Encyclopedia of DNA Elements (ENCODE) at the UCSC Genome Browser [ 13].
Comparing our findings with functional data from the Encyclopedia of DNA Elements (ENCODE) Project (16) [obtained through HaploReg (17) and the UCSC genome browser (18)] can help to predict the most likely functional SNPs (Fig. 1, Supplementary Material, Table S5).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com