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When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS. [ 2 ] Wilbanks and colleagues [ 3 ] is a survey of the ChIP-seq peak callers, and Bailey et al. [ 4 ] is a description of practical guidelines for peak calling in ChIP-seq data.
Schematic overview of the modular structure underlying procedures for gene set enrichment analysis. Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g ...
SMiLE-seq workflow. SMiLE-seq uses a microfluidic device into which transcription factors, which have been transcribed and translated in vitro, are loaded.Transcription factor samples (~0.3 ng) are modified by the addition of an enhanced green fluorescent protein (eGFP) tag and combined with both target double-stranded DNA molecules (~8 pmol) tagged with Cyanine Dye5 (Cy5) and a double ...
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
One analysis method, known as gene set enrichment analysis, identifies coregulated gene networks rather than individual genes that are up- or down-regulated in different cell populations. [1] Although microarray studies can reveal the relative amounts of different mRNAs in the cell, levels of mRNA are not directly proportional to the expression ...
It requires the usage of patient-derived xenografts for enrichment of ctDNA in blood for further analysis. After WGS, the method utilizes the tool Griffin [44] for inspection of local promoter coverage, nucleosome positioning, fragment size analysis, and composite transcription factor binding sites plus open chromatin sites of ctDNA reads. It ...
As with any scientific experiment, it is prudent to conduct RNA-Seq in a well controlled setting. If this is not possible or the study is a meta-analysis, another solution is to detect technical artifacts by inferring latent variables (typically principal component analysis or factor analysis) and subsequently correcting for these variables. [58]
The most commonly used method for identifying transcription factor binding sites is chromatin immunoprecipitation (ChIP). [89] This technique relies on chemical fixation of chromatin with formaldehyde, followed by co-precipitation of DNA and the transcription factor of interest using an antibody that specifically targets that protein.