Abstract:
:Transcription factors (TFs) binding to specific DNA sequences or motifs, are elementary to the regulation of transcription. The gene is regulated by a combination of TFs in close proximity. Analysis of co-TFs is an important problem in understanding the mechanism of transcriptional regulation. Recently, ChIP-seq in mapping TF provides a large amount of experimental data to analyze co-TFs. Several studies show that if two TFs are co-associated, the relative distance between TFs exhibits a peak-like distribution. In order to analyze co-TFs, we develop a novel method to evaluate the associated situation between TFs. We design an adjacency score based on ordered differences, which can illustrate co-TF binding affinities for motif analysis. For all candidate motifs, we calculate corresponding adjacency scores, and then list descending-order motifs. From these lists, we can find co-TFs for candidate motifs. On ChIP-seq datasets, our method obtains best AUC results on five datasets, 0.9432 for NMYC, 0.9109 for KLF4, 0.9006 for ZFX, 0.8892 for ESRRB, 0.8920 for E2F1. Our method has great stability on large sample datasets. AUC results of our method on all datasets are above 0.8.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Pan G,Tang J,Guo Fdoi
10.1038/srep43597subject
Has Abstractpub_date
2017-02-27 00:00:00pages
43597issn
2045-2322pii
srep43597journal_volume
7pub_type
杂志文章abstract::Surface plasmonics from metal nanoparticles have been demonstrated as an effective way of improving the performance of low-efficiency light emitters. However, reducing the inherent losses of the metal nanoparticles remains a challenge. Here we study the enhancement properties by Ag nanoparticles for InGaN/GaN quantum-...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep06392
更新日期:2014-09-22 00:00:00
abstract::Associations between cognitive decline and cerebral microbleeds (CMBs) have received increasing attention. An association between CMB distribution (deep or lobar) and cognitive decline has been reported, but these findings are controversial. We investigated the association between magnetic resonance imaging (MRI) find...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-73404-6
更新日期:2020-10-02 00:00:00
abstract::The development of effective central nervous system (CNS) drugs has been hampered by the lack of robust strategies to mimic the blood-brain barrier (BBB) and cerebrovascular impairments in vitro. Recent technological advancements in BBB modeling using induced pluripotent stem cells (iPSCs) allowed to overcome some of ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-52213-6
更新日期:2019-11-05 00:00:00
abstract::The prominent comprehensive properties of solid-solution- and intermetallic-based Ti alloys are derived from their diverse microstructures induced by multi-component alloying, which results in a chemical composition complexity. A cluster-plus-glue-atom model, characterizing the chemical short-range orders, was introdu...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-40302-5
更新日期:2019-03-04 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Scientific reports
pub_type: 已发布勘误
doi:10.1038/s41598-019-54657-2
更新日期:2019-11-25 00:00:00
abstract::Information concerning the pathogenic role of honey bee viruses in invasive species are still scarce. The aim of this investigation was to assess the presence of several honey bee viruses, such as Black Queen Cell Virus (BQCV), Kashmir Bee Virus (KBV), Slow Paralysis Virus (SPV), Sac Brood Virus (SBV), Israeli Acute P...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-46565-2
更新日期:2019-07-12 00:00:00
abstract::The ubiquitously expressed aryl hydrocarbon receptor (AhR) induces drug metabolizing enzymes as well as regulators of cell growth, differentiation and apoptosis. Certain AhR ligands promote atherosclerosis, an age-associated vascular disease. Therefore, we investigated the role of AhR in vascular functionality and agi...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep19618
更新日期:2016-01-21 00:00:00
abstract::The metabolic balance of the most extensive bioma on the Earth is a controversial topic of the global-change research. High ultraviolet radiation (UVR) levels by the shoaling of upper mixed layers and increasing atmospheric dust deposition from arid regions may unpredictably alter the metabolic state of marine oligotr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35892
更新日期:2016-10-24 00:00:00
abstract::Fire ants are widely studied, invasive and venomous arthropod pests. There is significant biomedical interest in immunotherapy against fire ant stings. However, mainly due to practical reasons, the physiological effects of envenomation has remained poorly characterized. The present study takes advantage of a recently-...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-32327-z
更新日期:2018-09-26 00:00:00
abstract::The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the pres...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-62195-5
更新日期:2020-03-30 00:00:00
abstract::Transgenic plants producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) are useful for pest control, but their efficacy is reduced when pests evolve resistance. Here we examined the mechanism of resistance to Bt toxin Cry1Ac in the laboratory-selected LF5 strain of the cotton bollworm, Helicov...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep07219
更新日期:2014-11-27 00:00:00
abstract::This study investigated the variation characteristics of micro-topography during successive erosive stages of water erosion: splash erosion (SpE), sheet erosion (ShE), and rill erosion (RE). Micro-topography was quantified using surface elevation change, soil roughness (SR) and multifractal model. Results showed that ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-21852-6
更新日期:2018-02-22 00:00:00
abstract::Upwelling off Vietnam in the South China Sea (SCS) and the Sumatra-Java upwelling in the Indian Ocean significantly modulate regional variation in climate. Although located in different hemispheres, these upwellings nearly concur during the boreal summer; both are the result of wind-induced Ekman divergence. Beyond se...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-40246-w
更新日期:2019-03-06 00:00:00
abstract::Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study,...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep07457
更新日期:2014-12-12 00:00:00
abstract::The P2X receptor family of ATP-gated cation channels are attractive drug targets for pain and inflammatory disease, but no subtype-selective agonists, and few partially selective agonists have been described to date. As proof-of-concept for the discovery of novel P2X receptor agonists, here we demonstrate the use of D...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-65169-9
更新日期:2020-05-19 00:00:00
abstract::New small molecules that regulate the step-wise differentiation of human pluripotent stem cells into dopaminergic neurons have been identified. The steroid, guggulsterone, was found to be the most effective inducer of neural stem cells into dopaminergic neurons. These neurons are extensively characterized and shown to...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep01463
更新日期:2013-01-01 00:00:00
abstract::In this letter, making use of real gait force profiles of healthy and patient groups with Parkinson disease which have different disease severity in terms of Hoehn-Yahr stage, we calculate various heuristic complexity measures of the recurrence quantification analysis (RQA). Using this technique, we are able to evince...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-27369-2
更新日期:2018-06-14 00:00:00
abstract::This study measured the effects of vitamin D (VD) supplementation on the underlying molecular pathways involved in renal and testicular damage induced by lead (Pb) toxicity. Thirty two adult male Wistar rats were divided equally into four groups that were treated individually or simultaneously, except the negative con...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-23258-w
更新日期:2018-03-19 00:00:00
abstract::We report the synthesis of single-crystal iron germanium nanowires via chemical vapor deposition without the assistance of any catalysts. The assembly of single-crystal FeGe2 nanowires with tetragonal C16 crystal structure shows anisotropic magnetic behavior along the radial direction or the growth axial direction, wi...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-05771-6
更新日期:2017-08-02 00:00:00
abstract::Although large populations feel fatigue, the standardized medicinal therapy is currently absent. In this study, we determined whether 5-aminolevulinic acid (5-ALA) supplementation alleviates the feeling of fatigue in healthy subjects who feel chronic physical tiredness. Males and females between ages of 20 and 64 who ...
journal_title:Scientific reports
pub_type: 杂志文章,随机对照试验
doi:10.1038/s41598-020-72763-4
更新日期:2020-09-29 00:00:00
abstract::Synapses are an early pathological target in many neurodegenerative diseases ranging from well-known adult onset conditions such as Alzheimer and Parkinson disease to neurodegenerative conditions of childhood such as spinal muscular atrophy (SMA) and neuronal ceroid lipofuscinosis (NCLs). However, the reasons why syna...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-12603-0
更新日期:2017-09-29 00:00:00
abstract::To evaluate the association of admission serum levels of 25(OH)D, parathormone and the related electrolytes with severity of illness and clinical outcomes in neurosurgical critically ill patients, serum levels of 25(OH)D, parathormone, calcium, magnesium, and phosphate, along with APACHE II score were measured for 210...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-21177-4
更新日期:2018-02-14 00:00:00
abstract::In this work, lamellar MnFe2O4 was successfully planted on a wood surface through the association of hydrogen bonds via the one-pot hydrothermal method. Simultaneously, the fluoroalkylsilane (FAS-17) on the surface of the MnFe2O4 layer formed long-chain or network macromolecules through a poly-condensation process and...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35549
更新日期:2016-10-17 00:00:00
abstract::Understanding the complex architecture, connectivity, and pathology of the human brain is a major application of magnetic resonance imaging (MRI). However, the cellular basis of MR signal is still poorly understood. The advent of MR microscopy (MRM) enables imaging biological samples at cellular resolution, helping to...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep08920
更新日期:2015-03-10 00:00:00
abstract::There is a significant need to develop antibacterial materials that could be applied locally and directly to the places surrounded by large amount of bacteria, in order to address the problems of bacterial antibiotic-resistance or irreversible biofilm formation. Hydrogels are thought to be suitable candidates due to t...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep07753
更新日期:2015-01-13 00:00:00
abstract::We report that misfolded cytosolic proteins can be cleared from mammalian cells by directing them to endoplasmic reticulum (ER). NAT1 R64W and Parkin R42P are naturally occurring misfolded variants of cytosolic enzymes that acetylate arylamines and ubiquitinate proteins, respectively. We demonstrate that proteasome in...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep12088
更新日期:2015-07-14 00:00:00
abstract::Early life overfeeding is associated with cognitive decline and anxiety-like behaviors in later life. It is not clear whether there are individual differences in the effects of early life overfeeding and what the underlying mechanistic pathways are. We investigated the long-lasting effects of small litter size, an exp...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-29595-0
更新日期:2018-07-26 00:00:00
abstract::TRAF-interacting protein with a forkhead-associated (FHA) domain (TIFA), originally identified as an adaptor protein of TRAF6, has recently been shown to be involved in innate immunity, induced by a pathogen-associated molecular pattern (PAMP). ADP-β-D-manno-heptose, a newly identified PAMP, binds to alpha-kinase 1 (A...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-61972-6
更新日期:2020-03-20 00:00:00
abstract::Invasive species are characterized by their ability to colonize new habitats and establish populations away from their native range. In this sense, these plants are expected to have plastic responses to adapt to the environmental pressures during the invasion process. Hence, the role of natural selection is essential ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-76922-5
更新日期:2020-11-18 00:00:00
abstract::The reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) can be achieved by ectopic expression of defined transcription factors (Oct3/4, Sox2, Klf4 and c-Myc). However, to date, some iPSCs have been generated using viral vectors; thus, unexpected insertional mutagenesis in the target cells...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep07323
更新日期:2014-12-04 00:00:00