39 research outputs found
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research
Genetic effects on gene expression across human tissues
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas
Expanded encyclopaedias of DNA elements in the human and mouse genomes
All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442
Genetic effects on gene expression across human tissues
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease
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Characterizing fluidized bed behavior by decomposition of chaotic phase space trajectories
Recent applications of chaotic time series analysis to gas fluidized beds have demonstrated that substantial information about fluidization conditions within the. bed can be extracted from voidage and pressure drop data. In this paper, a technique is presented to characterize fluidized bed behavior based on the crossings of the phase space trajectory through the principal component planes. Starting with either pressure drop or void fraction versus time data, time series embedding and principal component analysis is used to construct a phase space trajectory for the data. This trajectory characterizes the dynamical state of the bed. The technique presented decomposes the trajectory by sorting the orbits into types characteristic of different modes of bed behavior, such as emulsion phase fluctuations, bubbling, slugging, bubble coalescence, and de-fluidization. The basis for the method and the analysis of data from experiments in several fluidized beds will be presented. The overall goal of these studies is to improve the diagnostic and control of fossil energy fluidized bed processes
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Pneumatic solids feeder for coal gasification reactor
This invention is comprised of a pneumatic feeder system for a coal gasification reactor which includes one or more feeder tubes entering the reactor above the level of the particle bed inside the reactor. The tubes are inclined downward at their outer ends so that coal particles introduced into the tubes through an aperture at the top of the tubes slides downward away from the reactor and does not fall directly into the reactor. Pressurized gas introduced into, or resulting from ignition of recycled combustible gas in a chamber adjacent to the tube ends, propels the coal from the tube into the reactor volume and onto the particle bed. Leveling of the top of the bed is carried out by a bladed rotor mounted on the reactor stirring shaft. Coal is introduced into the tubes from containers above the tubes by means of rotary valves placed across supply conduits. This system avoids placement of feeder hardware in the plenum above the particle bed and keeps the coal from being excessively heated prior to reaching the particle bed
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A gas stream clean-up filter and method for forming same
A gas cleaning filter is formed in-situ within a vessel containing a fluidizable bed of granular material of a relatively large size fraction. A filter membrane provided by a porous metal or ceramic body or such a body supported a perforated screen on one side thereof is coated in-situ with a layer of the granular material from the fluidized bed by serially passing a bed-fluidizing gas stream through the bed of granular material and the membrane. The layer of granular material provides the filtering medium for the combined membrane-granular layer filter. The filter is not blinded by the granular material and provides for the removal of virtually all of the particulates from a process gas stream. The granular material can be at least partially provided by a material capable of chemically reacting with and removing sulfur compounds from the process gas stream. Low level radioactive waste containing organic material may be incinerated in a fluidized bed in communication with the described filter for removing particulates from the gaseous combustion products