10 research outputs found
Recommended from our members
Functional interpretation of single cell similarity maps.
We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration
Recommended from our members
Functional interpretation of single cell similarity maps.
We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration
Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity
Many mechanisms have been proposed
for how heightened aerobic glycolytic
metabolism fuels cancer pathogenicity, but there are still many unexplored
pathways. Here, we have performed metabolomic profiling to map glucose
incorporation into metabolic pathways upon transformation of mammary
epithelial cells by 11 commonly mutated human oncogenes. We show that
transformation of mammary epithelial cells by oncogenic stimuli commonly
shunts glucose-derived carbons into synthesis of sialic acid, a hexosamine
pathway metabolite that is converted to CMP-sialic acid by cytidine
monophosphate <i>N</i>-acetylneuraminic acid synthase (CMAS)
as a precursor to glycoprotein and glycolipid sialylation. We show
that CMAS knockdown leads to elevations in intracellular sialic acid
levels, a depletion of cellular sialylation, and alterations in the
expression of many cancer-relevant genes to impair breast cancer pathogenicity.
Our study reveals the heretofore unrecognized role of sialic acid
metabolism and protein sialylation in regulating the expression of
genes that maintain breast cancer pathogenicity
tanghaibao/goatools: GOATOOLS v0.7.6
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Added support for GOEA
Updated README
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Solar Wind Electrons Alphas and Protons (SWEAP) Investigation: Design of the Solar Wind and Coronal Plasma Instrument Suite for Solar Probe Plus
International audienceThe Solar Wind Electrons Alphas and Protons (SWEAP) Investigation on Solar Probe Plus is a four sensor instrument suite that provides complete measurements of the electrons and ionized helium and hydrogen that constitute the bulk of solar wind and coronal plasma. SWEAP consists of the Solar Probe Cup (SPC) and the Solar Probe Analyzers (SPAN). SPC is a Faraday Cup that looks directly at the Sun and measures ion and electron fluxes and flow angles as a function of energy. SPAN consists of an ion and electron electrostatic analyzer (ESA) on the ram side of SPP (SPAN-A) and an electron ESA on the anti-ram side (SPAN-B). The SPAN-A ion ESA has a time of flight section that enables it to sort particles by their mass/charge ratio, permitting differentiation of ion species. SPAN-A and -B are rotated relative to one another so their broad fields of view combine like the seams on a baseball to view the entire sky except for the region obscured by the heat shield and covered by SPC. Observations by SPC and SPAN produce the combined field of view and measurement capabilities required to fulfill the science objectives of SWEAP and Solar Probe Plus. SWEAP measurements, in concert with magnetic and electric fields, energetic particles, and white light contextual imaging will enable discovery and understanding of solar wind acceleration and formation, coronal and solar wind heating, and particle acceleration in the inner heliosphere of the solar system. SPC and SPAN are managed by the SWEAP Electronics Module (SWEM), which distributes power, formats onboard data products, and serves as a single electrical interface to the spacecraft. SWEAP data products include ion and electron velocity distribution functions with high energy and angular resolution. Full resolution data are stored within the SWEM, enabling high resolution observations of structures such as shocks, reconnection events, and other transient structures to be selected for download after the fact. This paper describes the implementation of the SWEAP Investigation, the driving requirements for the suite, expected performance of the instruments, and planned data products, as of mission preliminary design review