Mangan ME, Williams JM, Kuhn RM, Lathe WC 3rd (2009) The UCSC genome browser: what every molecular biologist should know . Curr Protoc Mol Biol Chapter 19 : Unit19.9 doi: 10.1002/0471142727.mb1909s88Mangan, M. E., Williams, J. M., Kuhn, R. M. & Lathe, W. C. The UCSC genome ...
A web-based tool that can be used in verification of coordinates is the UCSC Genome Browser In Silico PCR utility at: genome.ucsc.edu/cgi-bin/hgPcr. It is also important to make sure that amplicons are all approximately the same size, and that primer and pro...
map genomic assays to the genome, or gene expression assays to the transcriptome. A web-based tool that can be used in verification of coordinates is the UCSC Genome Browser In Silico PCR utility at: genome.ucsc.edu/cgi-bin/hgPcr. It is also important to make...
et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002). CAS PubMed PubMed Central Google Scholar Konieczna, A. et al. Differential expression of ABC transporters (MDR1, MRP1, BCRP) in developing human embryos. J. Mol. Histol 42, 567–574 (2011). CAS PubMed ...
The results are also available through several portals including the UCSC Genome Browser, Gitools (http://www.gitools.org/datasets/pancancer12), and MD Anderson’s Next-Generation Heatmaps (http://bioinformatics.mdanderson.org/main/TCGA/NGCHM). The NCI Clinical Proteomic Tumor Analysis Consortium...
The University of California Santa Cruz (UCSC) Genome Browser, build GRCh37, provided base pair positions, information about genomic regions and genes affected by CNVs, as well as known associated diseases (hg19). 2.5. Methylation Studies Methylation analysis was performed with the clinically ...
This algorithm also includes a bibliographic analysis that correlates miRNAs with different diseases, a graphic display with all the relevant functional information from the UCSC genome browser and a tracker for changes in the miRNA nomenclature [97]. In the latest version of microT (web server v...
Annotations can be gene-based (users can select the gene definition system; RefSeq, UCSC, ENSEMBL, GENCODE, etc.), region-based (transcription factor binding sites, DNAse I hypersensitivity sites, ENCODEmethylation sites, segmental duplication sites, DGV sites, etc.), filter-based (e.g., using...
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