scholarly journals Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

2013 ◽  
Vol 42 (5) ◽  
pp. 2976-2987 ◽  
Author(s):  
Pouya Kheradpour ◽  
Manolis Kellis
Keyword(s):  
Motif Discovery ◽  
Large Scale ◽  
De Novo ◽  
Specific Binding ◽  
Data Sets ◽  
Motif Analysis ◽  
Data Set ◽  
Number Of Factors ◽  
Cell Type Specific ◽  
Underlying Mechanisms

AbstractRecent advances in technology have led to a dramatic increase in the number of available transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of these data sets is an important step in understanding the underlying mechanisms of regulation. Here we provide a systematic motif analysis for 427 human ChIP-seq data sets using motifs curated from the literature and also discovered de novo using five established motif discovery tools. We use a systematic pipeline for calculating motif enrichment in each data set, providing a principled way for choosing between motif variants found in the literature and for flagging potentially problematic data sets. Our analysis confirms the known specificity of 41 of the 56 analyzed factor groups and reveals motifs of potential cofactors. We also use cell type-specific binding to find factors active in specific conditions. The resource we provide is accessible both for browsing a small number of factors and for performing large-scale systematic analyses. We provide motif matrices, instances and enrichments in each of the ENCODE data sets. The motifs discovered here have been used in parallel studies to validate the specificity of antibodies, understand cooperativity between data sets and measure the variation of motif binding across individuals and species.

scholarly journals A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yipu Zhang ◽  
Ping Wang
Keyword(s):  
High Throughput ◽  
Motif Discovery ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Es Cells ◽  
Motif Finding ◽  
Data Sets ◽  
Data Set ◽  
Binding Motifs ◽  
Motif Finding Algorithm

New high-throughput technique ChIP-seq, coupling chromatin immunoprecipitation experiment with high-throughput sequencing technologies, has extended the identification of binding locations of a transcription factor to the genome-wide regions. However, the most existing motif discovery algorithms are time-consuming and limited to identify binding motifs in ChIP-seq data which normally has the significant characteristics of large scale data. In order to improve the efficiency, we propose a fast cluster motif finding algorithm, named as FCmotif, to identify the(l, d)motifs in large scale ChIP-seq data set. It is inspired by the emerging substrings mining strategy to find the enriched substrings and then searching the neighborhood instances to construct PWM and cluster motifs in different length. FCmotif is not following the OOPS model constraint and can find long motifs. The effectiveness of proposed algorithm has been proved by experiments on the ChIP-seq data sets from mouse ES cells. The whole detection of the real binding motifs and processing of the full size data of several megabytes finished in a few minutes. The experimental results show that FCmotif has advantageous to deal with the(l, d)motif finding in the ChIP-seq data; meanwhile it also demonstrates better performance than other current widely-used algorithms such as MEME, Weeder, ChIPMunk, and DREME.

scholarly journals SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data

2013 ◽  
Vol 42 (5) ◽  
pp. e35-e35 ◽  
Author(s):  
Jun Ding ◽  
Haiyan Hu ◽  
Xiaoman Li
Keyword(s):  
Motif Discovery ◽  
De Novo ◽  
Data Sets ◽  
Random Data ◽  
Data Set ◽  
Binding Motifs ◽  
Gene Transcriptional Regulation ◽  
Novel Approach ◽  
De Novo Motif Discovery ◽  
Systematic Identification

Abstract The identification of transcription factor binding motifs is important for the study of gene transcriptional regulation. The chromatin immunoprecipitation (ChIP), followed by massive parallel sequencing (ChIP-seq) experiments, provides an unprecedented opportunity to discover binding motifs. Computational methods have been developed to identify motifs from ChIP-seq data, while at the same time encountering several problems. For example, existing methods are often not scalable to the large number of sequences obtained from ChIP-seq peak regions. Some methods heavily rely on well-annotated motifs even though the number of known motifs is limited. To simplify the problem, de novo motif discovery methods often neglect underrepresented motifs in ChIP-seq peak regions. To address these issues, we developed a novel approach called SIOMICS to de novo discover motifs from ChIP-seq data. Tested on 13 ChIP-seq data sets, SIOMICS identified motifs of many known and new cofactors. Tested on 13 simulated random data sets, SIOMICS discovered no motif in any data set. Compared with two recently developed methods for motif discovery, SIOMICS shows advantages in terms of speed, the number of known cofactor motifs predicted in experimental data sets and the number of false motifs predicted in random data sets. The SIOMICS software is freely available at http://eecs.ucf.edu/∼xiaoman/SIOMICS/SIOMICS.html.

scholarly journals Galaxy spin direction distribution in HST and SDSS show similar large-scale asymmetry

2020 ◽  
Vol 37 ◽  
Author(s):  
Lior Shamir
Keyword(s):  
Large Scale ◽  
Spiral Galaxies ◽  
Hubble Space Telescope ◽  
Gravitational Interaction ◽  
Large Data ◽  
Sloan Digital Sky Survey ◽  
Data Sets ◽  
Dipole Axis ◽  
Data Set ◽  
The Asymmetry

Abstract Several recent observations using large data sets of galaxies showed non-random distribution of the spin directions of spiral galaxies, even when the galaxies are too far from each other to have gravitational interaction. Here, a data set of $\sim8.7\cdot10^3$ spiral galaxies imaged by Hubble Space Telescope (HST) is used to test and profile a possible asymmetry between galaxy spin directions. The asymmetry between galaxies with opposite spin directions is compared to the asymmetry of galaxies from the Sloan Digital Sky Survey. The two data sets contain different galaxies at different redshift ranges, and each data set was annotated using a different annotation method. The results show that both data sets show a similar asymmetry in the COSMOS field, which is covered by both telescopes. Fitting the asymmetry of the galaxies to cosine dependence shows a dipole axis with probabilities of $\sim2.8\sigma$ and $\sim7.38\sigma$ in HST and SDSS, respectively. The most likely dipole axis identified in the HST galaxies is at $(\alpha=78^{\rm o},\delta=47^{\rm o})$ and is well within the $1\sigma$ error range compared to the location of the most likely dipole axis in the SDSS galaxies with $z>0.15$ , identified at $(\alpha=71^{\rm o},\delta=61^{\rm o})$ .

scholarly journals The Midlatitude Continental Convective Clouds Experiment (MC3E) sounding network: operations, processing and analysis

2015 ◽  
Vol 8 (1) ◽  
pp. 421-434 ◽  
Author(s):  
M. P. Jensen ◽  
T. Toto ◽  
D. Troyan ◽  
P. E. Ciesielski ◽  
D. Holdridge ◽  
...  
Keyword(s):  
Large Scale ◽  
Scale Model ◽  
Data Sets ◽  
Central Plains ◽  
Data Set ◽  
Convective Systems ◽  
Convective Clouds ◽  
Quality Checks ◽  
Network Operations ◽  
The Impact

Abstract. The Midlatitude Continental Convective Clouds Experiment (MC3E) took place during the spring of 2011 centered in north-central Oklahoma, USA. The main goal of this field campaign was to capture the dynamical and microphysical characteristics of precipitating convective systems in the US Central Plains. A major component of the campaign was a six-site radiosonde array designed to capture the large-scale variability of the atmospheric state with the intent of deriving model forcing data sets. Over the course of the 46-day MC3E campaign, a total of 1362 radiosondes were launched from the enhanced sonde network. This manuscript provides details on the instrumentation used as part of the sounding array, the data processing activities including quality checks and humidity bias corrections and an analysis of the impacts of bias correction and algorithm assumptions on the determination of convective levels and indices. It is found that corrections for known radiosonde humidity biases and assumptions regarding the characteristics of the surface convective parcel result in significant differences in the derived values of convective levels and indices in many soundings. In addition, the impact of including the humidity corrections and quality controls on the thermodynamic profiles that are used in the derivation of a large-scale model forcing data set are investigated. The results show a significant impact on the derived large-scale vertical velocity field illustrating the importance of addressing these humidity biases.

scholarly journals A fast methodology for large-scale focusing inversion of gravity and magnetic data using the structured model matrix and the 2-D fast Fourier transform

2020 ◽  
Vol 223 (2) ◽  
pp. 1378-1397
Author(s):  
Rosemary A Renaut ◽  
Jarom D Hogue ◽  
Saeed Vatankhah ◽  
Shuang Liu
Keyword(s):  
Fourier Transform ◽  
Fast Fourier Transform ◽  
Linear Systems ◽  
Large Scale ◽  
Surface Measurement ◽  
Magnetic Data ◽  
Uniform Grid ◽  
Data Sets ◽  
Inversion Algorithm ◽  
Data Set

SUMMARY We discuss the focusing inversion of potential field data for the recovery of sparse subsurface structures from surface measurement data on a uniform grid. For the uniform grid, the model sensitivity matrices have a block Toeplitz Toeplitz block structure for each block of columns related to a fixed depth layer of the subsurface. Then, all forward operations with the sensitivity matrix, or its transpose, are performed using the 2-D fast Fourier transform. Simulations are provided to show that the implementation of the focusing inversion algorithm using the fast Fourier transform is efficient, and that the algorithm can be realized on standard desktop computers with sufficient memory for storage of volumes up to size n ≈ 106. The linear systems of equations arising in the focusing inversion algorithm are solved using either Golub–Kahan bidiagonalization or randomized singular value decomposition algorithms. These two algorithms are contrasted for their efficiency when used to solve large-scale problems with respect to the sizes of the projected subspaces adopted for the solutions of the linear systems. The results confirm earlier studies that the randomized algorithms are to be preferred for the inversion of gravity data, and for data sets of size m it is sufficient to use projected spaces of size approximately m/8. For the inversion of magnetic data sets, we show that it is more efficient to use the Golub–Kahan bidiagonalization, and that it is again sufficient to use projected spaces of size approximately m/8. Simulations support the presented conclusions and are verified for the inversion of a magnetic data set obtained over the Wuskwatim Lake region in Manitoba, Canada.

scholarly journals Six years of total ozone column measurements from SCIAMACHY nadir observations

2009 ◽  
Vol 2 (1) ◽  
pp. 87-98 ◽  
Author(s):  
C. Lerot ◽  
M. Van Roozendael ◽  
J. van Geffen ◽  
J. van Gent ◽  
C. Fayt ◽  
...  
Keyword(s):  
Cross Sections ◽  
Total Ozone ◽  
Large Scale ◽  
European Space Agency ◽  
Data Sets ◽  
Data Set ◽  
Ozone Data ◽  
Space Agency ◽  
German Aerospace ◽  
The Impact

Abstract. Total O3 columns have been retrieved from six years of SCIAMACHY nadir UV radiance measurements using SDOAS, an adaptation of the GDOAS algorithm previously developed at BIRA-IASB for the GOME instrument. GDOAS and SDOAS have been implemented by the German Aerospace Center (DLR) in the version 4 of the GOME Data Processor (GDP) and in version 3 of the SCIAMACHY Ground Processor (SGP), respectively. The processors are being run at the DLR processing centre on behalf of the European Space Agency (ESA). We first focus on the description of the SDOAS algorithm with particular attention to the impact of uncertainties on the reference O3 absorption cross-sections. Second, the resulting SCIAMACHY total ozone data set is globally evaluated through large-scale comparisons with results from GOME and OMI as well as with ground-based correlative measurements. The various total ozone data sets are found to agree within 2% on average. However, a negative trend of 0.2–0.4%/year has been identified in the SCIAMACHY O3 columns; this probably originates from instrumental degradation effects that have not yet been fully characterized.

scholarly journals Collecting public RGB-D datasets for human daily activity recognition

2017 ◽  
Vol 14 (4) ◽  
pp. 172988141770907 ◽  
Author(s):  
Hanbo Wu ◽  
Xin Ma ◽  
Zhimeng Zhang ◽  
Haibo Wang ◽  
Yibin Li
Keyword(s):  
Activity Recognition ◽  
Daily Activity ◽  
Visual Cues ◽  
Large Scale ◽  
Hot Spot ◽  
Feature Representation ◽  
Data Sets ◽  
Activity Data ◽  
Data Set ◽  
Depth Motion Maps

Human daily activity recognition has been a hot spot in the field of computer vision for many decades. Despite best efforts, activity recognition in naturally uncontrolled settings remains a challenging problem. Recently, by being able to perceive depth and visual cues simultaneously, RGB-D cameras greatly boost the performance of activity recognition. However, due to some practical difficulties, the publicly available RGB-D data sets are not sufficiently large for benchmarking when considering the diversity of their activities, subjects, and background. This severely affects the applicability of complicated learning-based recognition approaches. To address the issue, this article provides a large-scale RGB-D activity data set by merging five public RGB-D data sets that differ from each other on many aspects such as length of actions, nationality of subjects, or camera angles. This data set comprises 4528 samples depicting 7 action categories (up to 46 subcategories) performed by 74 subjects. To verify the challengeness of the data set, three feature representation methods are evaluated, which are depth motion maps, spatiotemporal depth cuboid similarity feature, and curvature space scale. Results show that the merged large-scale data set is more realistic and challenging and therefore more suitable for benchmarking.

Characterising RDF data sets

2017 ◽  
Vol 44 (2) ◽  
pp. 203-229 ◽  
Author(s):  
Javier D Fernández ◽  
Miguel A Martínez-Prieto ◽  
Pablo de la Fuente Redondo ◽  
Claudio Gutiérrez
Keyword(s):  
Data Structures ◽  
Large Scale ◽  
Open Data ◽  
Structural Features ◽  
Data Sets ◽  
Data Set ◽  
Wide Range ◽  
Rdf Data ◽  
Description Framework ◽  
Resource Description

The publication of semantic web data, commonly represented in Resource Description Framework (RDF), has experienced outstanding growth over the last few years. Data from all fields of knowledge are shared publicly and interconnected in active initiatives such as Linked Open Data. However, despite the increasing availability of applications managing large-scale RDF information such as RDF stores and reasoning tools, little attention has been given to the structural features emerging in real-world RDF data. Our work addresses this issue by proposing specific metrics to characterise RDF data. We specifically focus on revealing the redundancy of each data set, as well as common structural patterns. We evaluate the proposed metrics on several data sets, which cover a wide range of designs and models. Our findings provide a basis for more efficient RDF data structures, indexes and compressors.

scholarly journals Variability in the Power Spectrum of Solar Five-Minute Oscillations

1983 ◽  
Vol 66 ◽  
pp. 411-425
Author(s):  
Frank Hill ◽  
Juri Toomre ◽  
Laurence J. November
Keyword(s):  
Large Scale ◽  
Solar Rotation ◽  
Temporal Frequency ◽  
Power Spectra ◽  
Giant Cells ◽  
Spectral Lines ◽  
Data Sets ◽  
Data Set ◽  
Temporal Sampling ◽  
Velocity Changes

AbstractTwo-dimensional power spectra of solar five-minute oscillations display prominent ridge structures in (k, ω) space, where k is the horizontal wavenumber and ω is the temporal frequency. The positions of these ridges in k and ω can be used to probe temperature and velocity structures in the subphotosphere. We have been carrying out a continuing program of observations of five-minute oscillations with the diode array instrument on the vacuum tower telescope at Sacramento Peak Observatory (SPO). We have sought to establish whether power spectra taken on separate days show shifts in ridge locations; these may arise from different velocity and temperature patterns having been brought into our sampling region by solar rotation. Power spectra have been obtained for six days of observations of Doppler velocities using the Mg I λ5173 and Fe I λ5434 spectral lines. Each data set covers 8 to 11 hr in time and samples a region 256″ × 1024″ in spatial extent, with a spatial resolution of 2″ and temporal sampling of 65 s. We have detected shifts in ridge locations between certain data sets which are statistically significant. The character of these displacements when analyzed in terms of eastward and westward propagating waves implies that changes have occurred in both temperature and horizontal velocity fields underlying our observing window. We estimate the magnitude of the velocity changes to be on the order of 100 m s -1; we may be detecting the effects of large-scale convection akin to giant cells.

scholarly journals Dynamic spatio-temporal generation of large-scale synthetic gridded precipitation: with improved spatial coherence of extremes

2019 ◽  
Vol 34 (9) ◽  
pp. 1369-1383 ◽  
Author(s):  
Dirk Diederen ◽  
Ye Liu
Keyword(s):  
Large Scale ◽  
Spatial Coherence ◽  
Original Data ◽  
Return Level ◽  
Data Sets ◽  
Large Set ◽  
Precipitation Data ◽  
Data Set ◽  
Spatio Temporal ◽  
Synthetic Precipitation

Abstract With the ongoing development of distributed hydrological models, flood risk analysis calls for synthetic, gridded precipitation data sets. The availability of large, coherent, gridded re-analysis data sets in combination with the increase in computational power, accommodates the development of new methodology to generate such synthetic data. We tracked moving precipitation fields and classified them using self-organising maps. For each class, we fitted a multivariate mixture model and generated a large set of synthetic, coherent descriptors, which we used to reconstruct moving synthetic precipitation fields. We introduced randomness in the original data set by replacing the observed precipitation fields in the original data set with the synthetic precipitation fields. The output is a continuous, gridded, hourly precipitation data set of a much longer duration, containing physically plausible and spatio-temporally coherent precipitation events. The proposed methodology implicitly provides an important improvement in the spatial coherence of precipitation extremes. We investigate the issue of unrealistic, sudden changes on the grid and demonstrate how a dynamic spatio-temporal generator can provide spatial smoothness in the probability distribution parameters and hence in the return level estimates.

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