Abstract:
BACKGROUND:Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase sequencing libraries. The processing of these sequencing techniques involves library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from each genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such complex analysis often relies on multiple programs and is therefore a challenge for those without programming skills. RESULTS:We developed DEBrowser as an R bioconductor project to interactively visualize every step of the differential analysis, without programming. The application provides a rich and interactive web based graphical user interface built on R's shiny infrastructure. DEBrowser allows users to visualize data with various types of graphs that can be explored further by selecting and re-plotting any desired subset of data. Using the visualization approaches provided, users can determine and correct technical variations such as batch effects and sequencing depth that affect differential analysis. We show DEBrowser's ease of use by reproducing the analysis of two previously published data sets. CONCLUSIONS:DEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Kucukural A,Yukselen O,Ozata DM,Moore MJ,Garber Mdoi
10.1186/s12864-018-5362-xsubject
Has Abstractpub_date
2019-01-05 00:00:00pages
6issue
1issn
1471-2164pii
10.1186/s12864-018-5362-xjournal_volume
20pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06955-7
更新日期:2020-08-14 00:00:00
abstract:BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3797-0
更新日期:2017-05-23 00:00:00
abstract:BACKGROUND:Selenium (Se) is a trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine (SeU). Selenophosphate synthetase (SelD) is required for both utilization traits. However, previous research also revealed SelDs in two organisms lacking Sec and SeU, suggest...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-251
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs affecting the expression of target genes via translational repression or mRNA degradation mechanisms. With the increasing availability of mRNA and miRNA expression data, it might be possible to assess functional targets using the fact that a miRNA might down-regul...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-218
更新日期:2009-05-12 00:00:00
abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1679-x
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-169
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression system...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-92
更新日期:2008-02-25 00:00:00
abstract:BACKGROUND:The ability to identify regions of the genome inherited with a dominant trait in one or more families has become increasingly valuable with the wide availability of high throughput sequencing technology. While a number of methods exist for mapping of homozygous variants segregating with recessive traits in c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1360-4
更新日期:2015-03-10 00:00:00
abstract:BACKGROUND:CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-283
更新日期:2010-05-05 00:00:00
abstract:BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-565
更新日期:2014-07-05 00:00:00
abstract:BACKGROUND:Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. RESULTS:Here, we present eight new Ptr isolate g...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4680-3
更新日期:2018-04-23 00:00:00
abstract:BACKGROUND:Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6360-3
更新日期:2019-12-19 00:00:00
abstract:BACKGROUND:Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S9-S12
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-693
更新日期:2010-12-07 00:00:00
abstract:BACKGROUND:The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-58
更新日期:2012-02-03 00:00:00
abstract:BACKGROUND:There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-135
更新日期:2006-06-02 00:00:00
abstract:BACKGROUND:Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-98
更新日期:2005-07-13 00:00:00
abstract:BACKGROUND:Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-722
更新日期:2012-12-23 00:00:00
abstract:BACKGROUND:Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5499-2
更新日期:2019-02-07 00:00:00
abstract:BACKGROUND:Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-305
更新日期:2008-06-26 00:00:00
abstract:BACKGROUND:The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. RESULTS:In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-370
更新日期:2014-05-15 00:00:00
abstract:BACKGROUND:Adaptive divergence driven by environmental heterogeneity has long been a fascinating topic in ecology and evolutionary biology. The study of the genetic basis of adaptive divergence has, however, been greatly hampered by a lack of genomic information. The recent development of transcriptome sequencing provi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-149
更新日期:2012-04-24 00:00:00
abstract:BACKGROUND:Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disea...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1295-9
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-289
更新日期:2011-06-03 00:00:00
abstract:BACKGROUND:Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. RESULTS:We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-454
更新日期:2010-07-28 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3114-3
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:Atlantic salmon have been subject to domestication for approximately ten generations, beginning in the early 1970s. This process of artificial selection will have created various genetic differences between wild and farmed stocks. Each year, hundreds of thousands of farmed fish escape into the wild. These es...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-884
更新日期:2014-10-09 00:00:00
abstract:BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2541-5
更新日期:2016-03-08 00:00:00
abstract:BACKGROUND:The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential roles in contributing to their overall health and production performance. In the present study, RNA se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6320-y
更新日期:2019-12-12 00:00:00
abstract:BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-948
更新日期:2014-11-01 00:00:00