Abstract：
:The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Kondili M,Fust A,Preussner J,Kuenne C,Braun T,Looso Mdoi
10.1038/s41598-017-02464-ysubject
Has Abstractpub_date
2017-06-01 00:00:00pages
2593issue
1issn
2045-2322pii
10.1038/s41598-017-02464-yjournal_volume
7pub_type
杂志文章abstract：:Lonicera japonica Thunb, rich in chlorogenic acid (CHA), is used for viral upper respiratory tract infection treatment caused by influenza virus, parainfluenza virus, and respiratory syncytial virus, ect in China. It was reported that CHA reduced serum hepatitis B virus level and death rate of influenza virus-infected...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep45723
更新日期：2017-04-10 00:00:00
abstract：:The main feature of the present numerical model is to explore the behavior of Maxwell nanoliquid moving within two horizontal rotating disks. The disks are stretchable and subjected to a magnetic field in axial direction. The time dependent characteristics of thermal conductivity have been considered to scrutinize the...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-74096-8
更新日期：2020-10-13 00:00:00
abstract：:Accurate measurements of autonomic nerve regulation in heart failure (HF) were unresolved. The discriminating performance of deceleration and acceleration capacities of heart rate in HF was evaluated in 130 HF patients and 212 controls. Acceleration capacity and deceleration capacity were independent risk factors for ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep23617
更新日期：2016-03-23 00:00:00
abstract：:The tibial tuberosity-trochlear groove (TT-TG) distance is a radiographic measurement that is used to quantify malalignment of the patellofemoral joint (PFJ) in cross-sectional imaging. There is an ongoing debate about the impact of the TT-TG-distance on lateral patellar instability and the initiating of cartilage deg...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-72299-7
更新日期：2020-09-18 00:00:00
abstract：:Continuous, as opposed to pulsatile, delivery of hypothalamic gonadotropin-releasing hormone (GnRH) leads to a marked decrease in secretion of pituitary gonadotropins LH and FSH and impairment of reproductive function. Here we studied the expression profile of gonadotropin subunit and GnRH receptor genes in rat pituit...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-56480-1
更新日期：2019-12-27 00:00:00
abstract：:Following retinal degeneration, retinal remodeling can cause neuronal microcircuits to undergo structural alterations, which particularly affect the dendrites of bipolar cells. However, the mechanisms and functional consequences of such changes remain unclear. Here, we used Royal College of Surgeon (RCS) rats as a mod...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-01261-x
更新日期：2017-04-21 00:00:00
abstract：:Perinatal depression involves interplay between individual chronic and acute disease burdens, biological and psychosocial environmental and behavioural factors. Here we explored the predictive potential of specific psycho-socio-demographic characteristics for antenatal and postpartum depression symptoms and contributi...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-30874-z
更新日期：2018-08-24 00:00:00
abstract：:The reduced micromorphic model (RMM) is used to study the effect of the applied force on a hemisphere made of phononic crystals that belongs to the metamaterials group. The strain tensor, the micro-strain tensor and the coupling between them are the kinematic relations used to measure the deformation and micro-deforma...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-59696-8
更新日期：2020-02-18 00:00:00
abstract：:Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-16269-6
更新日期：2017-12-11 00:00:00
abstract：:The therapeutic potential of nonthermal plasma for cancer treatment has been reported recently. The heterogeneity of cancer cells need to be addressed to design effective anticancer treatments. Here, we show that treatment with nonthermal atmospheric-pressure plasma dissolved in a liquid (liquid plasma) induces oxidat...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep29020
更新日期：2016-07-01 00:00:00
abstract：:Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-65277-6
更新日期：2020-05-26 00:00:00
abstract：:Salinization is having a major impact on wetlands and its biota worldwide. Specifically, many migratory animals that rely on wetlands are increasingly exposed to elevated salinity on their nonbreeding grounds. Experimental evidence suggests that physiological challenges associated with increasing salinity may disrupt ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-07258-w
更新日期：2017-07-31 00:00:00
abstract：:The generation of novelty is central to any creative endeavor. Novelty generation and the relationship between novelty and individual hedonic value have long been subjects of study in social psychology. However, few studies have utilized large-scale datasets to quantitatively investigate these issues. Here we consider...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep02758
更新日期：2013-09-26 00:00:00
abstract：:Agricultural soil is often subjected to waterlogging after heavy rainfalls, resulting in sharp and explosive increases in the emission of nitrous oxide (N2O), an important greenhouse gas primarily released from agricultural soil ecosystems. Previous studies on waterlogged soil examined the abundance of denitrifiers bu...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-00953-8
更新日期：2017-04-11 00:00:00
abstract：:The objective of this study was to examine the relationship between sleep duration and ischemic and hemorrhagic stroke in a community-based cohort. The current analysis included 95,023 Chinese participants who were free of stroke at the baseline survey (2006-2007). Cox proportional hazards models were used to calculat...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep33664
更新日期：2016-09-16 00:00:00
abstract：:Wide-angle optical systems play a vital role in imaging applications and have been researched for many years. In traditional lenses, attaining a wide field of view (FOV) by using a single optical component is difficult because these lenses have crucial aberrations. In this study, we developed a wide-angle metalens wit...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-72668-2
更新日期：2020-09-24 00:00:00
abstract：:The taxa of Astragalus section Hymenostegis are an important element of mountainous and steppe habitats in Southwest Asia. A phylogenetic hypothesis of sect. Hymenostegis has been obtained from nuclear ribosomal DNA internal transcribed spacer (ITS) and plastid ycf1 sequences of up to 303 individuals from 106 species,...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-14614-3
更新日期：2017-10-25 00:00:00
abstract：:Functional neuroimaging, using genetically-encoded Ca2+ sensors in larval zebrafish, offers a powerful combination of high spatiotemporal resolution and higher vertebrate relevance for quantitative neuropharmacological profiling. Here we use zebrafish larvae with pan-neuronal expression of GCaMP6s, combined with light...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-06646-6
更新日期：2017-07-26 00:00:00
abstract：:Tumors are characterized by a rigid, highly cross-linked extracellular matrix (ECM), which impedes homogeneous drug distribution and potentially protects malignant cells from exposure to therapeutics. Lysyl oxidases are major contributors to tissue stiffness and the elevated expression of these enzymes observed in mos...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep17576
更新日期：2015-12-01 00:00:00
abstract：:Various sea foods including fish, shellfish and shrimp were collected from different coastal areas of Fujian in China, and their Pb species characteristics were investigated in detail. The results indicated that there are two different species characteristics of Pb existing in sea food samples. About half of samples w...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep33294
更新日期：2016-09-14 00:00:00
abstract：:Atrial fibrillation (AF) is known to cause adverse remodeling of left atrium (LA). Radiofrequency catheter ablation (RFCA) of AF is associated with decrease in LA volume. However, the impact of RFCA on left atrial appendage (LAA) volume and hemodynamic function is not fully understood. We analyzed 123 patients who und...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-26212-y
更新日期：2018-05-18 00:00:00
abstract：:Algicidal microbes could effectively remove the harmful algae from the waters. In this study, we were concerned with the ecological influence of an algicide extracted from Streptomyces alboflavus RPS, which could completely lyse the Phaeocystis globosa cells within two days. In microcosms, 4 μg/mL of the microbial alg...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep20081
更新日期：2016-02-05 00:00:00
abstract：:Brain tumors are fast proliferating and destructive within the brain microenvironment. Effective chemotherapeutic strategies are currently lacking which combat this deadly disease curatively. The glioma-specific chloride ion channel represents a specific target for therapy. Chlorotoxin (CTX), a peptide derived from sc...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19799
更新日期：2016-02-02 00:00:00
abstract：:Tissue fibrosis underlies the majority of human mortality to date with close to half of all reported deaths having a fibrotic etiology. The progression of fibrosis is very complex and reputed irreversible once established. Although some preventive options are being reported, therapeutic options are still scarce and in...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-67514-4
更新日期：2020-06-30 00:00:00
abstract：:Solid-state spin-based qubits offer good prospects for scaling based on their long coherence times and nexus to large-scale electronic scale-up technologies. However, high-threshold quantum error correction requires a two-dimensional qubit array operating in parallel, posing significant challenges in fabrication and c...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-13308-0
更新日期：2017-10-17 00:00:00
abstract：:Pain is a highly unpleasant sensory and emotional experience, and no objective diagnosis test exists to assess it. In clinical practice there are two main methods for the estimation of pain, a patient's self-report and clinical judgement. However, these methods are highly subjective and the need of biomarkers to measu...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-42098-w
更新日期：2019-04-04 00:00:00
abstract：:To improve estimates of the long-term response of the marine carbon system to climate change a better understanding of the seasonal and interannual variability is needed. We use high-frequency multi-year data at three locations identified as climate change hotspots: two sites located close to South Pacific boundary cu...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-44109-2
更新日期：2019-05-20 00:00:00
abstract：:Organic-inorganic halide perovskite nanocrystals or quantum dots (PQDs) are excellent candidates for optoelectronic applications, such as lasers, solar cells, light emitting diodes, and single photon sources. However, the potential applications of PQDs can expand once the photoluminescence, and in particular, the blin...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-58926-3
更新日期：2020-02-07 00:00:00
abstract：:Transjugular intrahepatic portosystemic shunt (TIPS) can treat portal hypertensive complications and modifies hepatic hemodynamics. Modification of liver perfusion can alter contrast enhancement dynamics of liver nodules. This study investigated the diagnostic performance of contrast-enhanced ultrasound (CEUS) to diag...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-77801-9
更新日期：2020-11-26 00:00:00
abstract：:Pilonidal sinus disease (PSD) is increasing globally. A recent meta-analysis and merged-data analysis showed that recurrence rates in PSD depend essentially on follow-up time and specific surgical procedures. However, the global distribution of surgical approaches and respective recurrence rates have never been studie...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-51159-z
更新日期：2019-10-22 00:00:00
