We are analyzing https://link.springer.com/article/10.1186/1471-2164-15-284.

Title:
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases | BMC Genomics
Description:
Background Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.
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Keywords {🔍}

pubmed, article, google, scholar, regions, file, ngsplot, data, cas, figure, central, genome, coverage, files, gene, bam, tet, genomic, ngs, enrichment, alignment, cell, size, sequencing, additional, samples, tabix, time, rnaseq, human, sites, enhancers, million, bigwig, chipseq, liu, functional, rle, cells, analysis, program, exons, user, hkme, index, dna, elements, alignments, marks, region,

Topics {✒️}

org/packages/release/bioc/html/rsamtools de/users/anders/htseq/doc/index xiaochuan liu & eric nestler cg di-nucleotide percentages tab-delimited text file tab-delimited text files generic tab-delimited files tissue/cell-type specific expression article download pdf google search technology include chip-seq article published online house rna-seq dataset high-throughput assays mediator establish super-enhancers full size image web-based genome browsers cg-rich regions due genomic annotation databases open access license pastor wa multiple chip-seq samples rna-seq sequence alignments friedman brain institute sequence alignment/map format integrating genomic databases drosophila chromatin occur kent wj rna-seq quality control gene/transcript ids/names perform location-based classifications cpg-related promoters [61] 5hmc chip-seq data full access article shen human postmortem tissue chromatin state dynamics open-source project technology transfer office privacy choices/manage cookies generation sequencing revolution authors’ original file sequence read archive cis-regulatory sequences short read aligner important research topic generation sequencing technology enrichment-based epigenomic data called “bivalent” domains cocaine-induced plasticity

Questions {❓}

Does this mark show any co-occurrence with other marks and do their co-enrichments define gene modules?
If a ranked gene list is obtained based on the enrichment of this mark, does it associate with gene expression?
Stan AD, Ghose S, Gao XM, Roberts RC, Lewis-Amezcua K, Hatanpaa KJ, Tamminga CA: Human postmortem tissue: what quality markers matter?
What is the enrichment of this mark at transcriptional start sites (TSSs) as well as several Kb up- and down-stream?

Schema {🗺️}

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         Visualization
         Epigenomics
         Data mining
         Genomic databases
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         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      name:Ningyi Shao
      affiliation:
            name:Icahn School of Medicine at Mount Sinai
            address:
               name:Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
               type:PostalAddress
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      name:Xiaochuan Liu
      affiliation:
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            address:
               name:Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
               type:PostalAddress
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      affiliation:
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      name:Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
      name:Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA

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