当前位置： SCI文献检索 > Nature Communications期刊下所有文献 > Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases.

Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases.

Abstract：

:In silico quantification of cell proportions from mixed-cell transcriptomics data (deconvolution) requires a reference expression matrix, called basis matrix. We hypothesize that matrices created using only healthy samples from a single microarray platform would introduce biological and technical biases in deconvolution. We show presence of such biases in two existing matrices, IRIS and LM22, irrespective of deconvolution method. Here, we present immunoStates, a basis matrix built using 6160 samples with different disease states across 42 microarray platforms. We find that immunoStates significantly reduces biological and technical biases. Importantly, we find that different methods have virtually no or minimal effect once the basis matrix is chosen. We further show that cellular proportion estimates using immunoStates are consistently more correlated with measured proportions than IRIS and LM22, across all methods. Our results demonstrate the need and importance of incorporating biological and technical heterogeneity in a basis matrix for achieving consistently high accuracy.

journal_name

Nat Commun

journal_title

Nature communications

authors

Vallania F,Tam A,Lofgren S,Schaffert S,Azad TD,Bongen E,Haynes W,Alsup M,Alonso M,Davis M,Engleman E,Khatri P

doi

10.1038/s41467-018-07242-6

subject

Has Abstract

pub_date

2018-11-09 00:00:00

pages

4735

issue

1

issn

2041-1723

pii

10.1038/s41467-018-07242-6

journal_volume

9

pub_type

杂志文章

相关文献

Nature Communications文献大全
  • A new protein complex promoting the assembly of Rad51 filaments.

    abstract：:During homologous recombination, eukaryotic RecA homologue Rad51 assembles into a nucleoprotein filament on single-stranded DNA to catalyse homologous pairing and DNA-strand exchange with a homologous template. Rad51 nucleoprotein filaments are highly dynamic and regulated via the coordinated actions of various access...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2678

    authors： Sasanuma H,Tawaramoto MS,Lao JP,Hosaka H,Sanda E,Suzuki M,Yamashita E,Hunter N,Shinohara M,Nakagawa A,Shinohara A

    更新日期：2013-01-01 00:00:00

  • Early Cretaceous chalks from the North Sea giving evidence for global change.

    abstract：:Among calcareous nannofossils, important primary producers in Jurassic and Cretaceous oceans, nannoconids were carbonate rock-forming organisms. During the late Barremian and early Aptian (~126 to 122 million years ago), nannoconids went through a crisis culminating during the Oceanic Anoxic Event 1a. Here we present ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2698

    authors： Mutterlose J,Bottini C

    更新日期：2013-01-01 00:00:00

  • A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo.

    abstract：:To expand the toolbox of imaging in living cells, we have engineered a single-chain variable fragment binding the linear HA epitope with high affinity and specificity in vivo. The resulting probe, called the HA frankenbody, can light up in multiple colors HA-tagged nuclear, cytoplasmic, membrane, and mitochondrial pro...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-10846-1

    authors： Zhao N,Kamijo K,Fox PD,Oda H,Morisaki T,Sato Y,Kimura H,Stasevich TJ

    更新日期：2019-07-03 00:00:00

  • Phosphatidylserine exposure is required for ADAM17 sheddase function.

    abstract：:ADAM17, a prominent member of the 'Disintegrin and Metalloproteinase' (ADAM) family, controls vital cellular functions through cleavage of transmembrane substrates. Here we present evidence that surface exposure of phosphatidylserine (PS) is pivotal for ADAM17 to exert sheddase activity. PS exposure is tightly coupled...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms11523

    authors： Sommer A,Kordowski F,Büch J,Maretzky T,Evers A,Andrä J,Düsterhöft S,Michalek M,Lorenzen I,Somasundaram P,Tholey A,Sönnichsen FD,Kunzelmann K,Heinbockel L,Nehls C,Gutsmann T,Grötzinger J,Bhakdi S,Reiss K

    更新日期：2016-05-10 00:00:00

  • Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans.

    abstract：:Paternal epigenetic inheritance is gaining attention for its growing medical relevance. However, the form in which paternal epigenetic information is transmitted to offspring and how it influences offspring development remain poorly understood. Here we show that in C. elegans, sperm-inherited chromatin states transmit...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-09141-w

    authors： Kaneshiro KR,Rechtsteiner A,Strome S

    更新日期：2019-03-20 00:00:00

  • Tau association with synaptic vesicles causes presynaptic dysfunction.

    abstract：:Tau is implicated in more than 20 neurodegenerative diseases, including Alzheimer's disease. Under pathological conditions, Tau dissociates from axonal microtubules and missorts to pre- and postsynaptic terminals. Patients suffer from early synaptic dysfunction prior to Tau aggregate formation, but the underlying mech...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15295

    authors： Zhou L,McInnes J,Wierda K,Holt M,Herrmann AG,Jackson RJ,Wang YC,Swerts J,Beyens J,Miskiewicz K,Vilain S,Dewachter I,Moechars D,De Strooper B,Spires-Jones TL,De Wit J,Verstreken P

    更新日期：2017-05-11 00:00:00

  • High-coherence electron bunches produced by femtosecond photoionization.

    abstract：:With the development of ultrafast electron and X-ray sources it is becoming possible to study structural dynamics with atomic-level spatial and temporal resolution. Because of their short mean free path, electrons are particularly well suited for investigating surfaces and thin films, such as the challenging and impor...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2700

    authors： Engelen WJ,van der Heijden MA,Bakker DJ,Vredenbregt EJ,Luiten OJ

    更新日期：2013-01-01 00:00:00

  • Compaction of quasi-one-dimensional elastoplastic materials.

    abstract：:Insight into crumpling or compaction of one-dimensional objects is important for understanding biopolymer packaging and designing innovative technological devices. By compacting various types of wires in rigid confinements and characterizing the morphology of the resulting crumpled structures, here, we report how fric...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15568

    authors： Shaebani MR,Najafi J,Farnudi A,Bonn D,Habibi M

    更新日期：2017-06-06 00:00:00

  • Genetic variation at MECOM, TERT, JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms.

    abstract：:Clonal proliferation in myeloproliferative neoplasms (MPN) is driven by somatic mutations in JAK2, CALR or MPL, but the contribution of inherited factors is poorly characterized. Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms7691

    authors： Tapper W,Jones AV,Kralovics R,Harutyunyan AS,Zoi K,Leung W,Godfrey AL,Guglielmelli P,Callaway A,Ward D,Aranaz P,White HE,Waghorn K,Lin F,Chase A,Baxter EJ,Maclean C,Nangalia J,Chen E,Evans P,Short M,Jack A,Wal

    更新日期：2015-04-07 00:00:00

  • Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy.

    abstract：:Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it ha...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2204

    authors： Borgia A,Wensley BG,Soranno A,Nettels D,Borgia MB,Hoffmann A,Pfeil SH,Lipman EA,Clarke J,Schuler B

    更新日期：2012-01-01 00:00:00

  • Reversing the charge transfer between platinum and sulfur-doped carbon support for electrocatalytic hydrogen evolution.

    abstract：:Metal-support interaction is of great significance for catalysis as it can induce charge transfer between metal and support, tame electronic structure of supported metals, impact adsorption energy of reaction intermediates, and eventually change the catalytic performance. Here, we report the metal size-dependent charg...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-12851-w

    authors： Yan QQ,Wu DX,Chu SQ,Chen ZQ,Lin Y,Chen MX,Zhang J,Wu XJ,Liang HW

    更新日期：2019-10-31 00:00:00

  • Control of chrysanthemum flowering through integration with an aging pathway.

    abstract：:Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmN...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-00812-0

    authors： Wei Q,Ma C,Xu Y,Wang T,Chen Y,Lü J,Zhang L,Jiang CZ,Hong B,Gao J

    更新日期：2017-10-10 00:00:00

  • Virus-borne mini-CRISPR arrays are involved in interviral conflicts.

    abstract：:CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome-all spacers contained in a microbiome-associated with hyperthermophilic arc...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-13205-2

    authors： Medvedeva S,Liu Y,Koonin EV,Severinov K,Prangishvili D,Krupovic M

    更新日期：2019-11-15 00:00:00

  • A troodontid dinosaur from the latest Cretaceous of India.

    abstract：:Troodontid dinosaurs share a close ancestry with birds and were distributed widely across Laurasia during the Cretaceous. Hundreds of occurrences of troodontid bones, and their highly distinctive teeth, are known from North America, Europe and Asia. Thus far, however, they remain unknown from Gondwanan landmasses. Her...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2716

    authors： Goswami A,Prasad GV,Verma O,Flynn JJ,Benson RB

    更新日期：2013-01-01 00:00:00

  • High susceptibility to fatty liver disease in two-pore channel 2-deficient mice.

    abstract：:Endolysosomal organelles play a key role in trafficking, breakdown and receptor-mediated recycling of different macromolecules such as low-density lipoprotein (LDL)-cholesterol, epithelial growth factor (EGF) or transferrin. Here we examine the role of two-pore channel (TPC) 2, an endolysosomal cation channel, in thes...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms5699

    authors： Grimm C,Holdt LM,Chen CC,Hassan S,Müller C,Jörs S,Cuny H,Kissing S,Schröder B,Butz E,Northoff B,Castonguay J,Luber CA,Moser M,Spahn S,Lüllmann-Rauch R,Fendel C,Klugbauer N,Griesbeck O,Haas A,Mann M,Bracher F,T

    更新日期：2014-08-21 00:00:00

  • Voltage tunability of single-spin states in a quantum dot.

    abstract：:Single spins in the solid state offer a unique opportunity to store and manipulate quantum information, and to perform quantum-enhanced sensing of local fields and charges. Optical control of these systems using techniques developed in atomic physics has yet to exploit all the advantages of the solid state. Here we de...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2519

    authors： Bennett AJ,Pooley MA,Cao Y,Sköld N,Farrer I,Ritchie DA,Shields AJ

    更新日期：2013-01-01 00:00:00

  • Discontinuation of anti-VEGF cancer therapy promotes metastasis through a liver revascularization mechanism.

    abstract：:The impact of discontinuation of anti-VEGF cancer therapy in promoting cancer metastasis is unknown. Here we show discontinuation of anti-VEGF treatment creates a time-window of profound structural changes of liver sinusoidal vasculatures, exhibiting hyper-permeability and enlarged open-pore sizes of the fenestrated e...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12680

    authors： Yang Y,Zhang Y,Iwamoto H,Hosaka K,Seki T,Andersson P,Lim S,Fischer C,Nakamura M,Abe M,Cao R,Skov PV,Chen F,Chen X,Lu Y,Nie G,Cao Y

    更新日期：2016-09-01 00:00:00

  • The effect of crystallite size on pressure amplification in switchable porous solids.

    abstract：:Negative gas adsorption (NGA) in ordered mesoporous solids is associated with giant contractive structural transitions traversing through metastable states. Here, by systematically downsizing the crystal dimensions of a mesoporous MOF (DUT-49) from several micrometers to less than 200 nm, counterintuitive NGA phenomen...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03979-2

    authors： Krause S,Bon V,Senkovska I,Többens DM,Wallacher D,Pillai RS,Maurin G,Kaskel S

    更新日期：2018-04-20 00:00:00

  • The halogen bond with isocyano carbon reduces isocyanide odor.

    abstract：:Predominantly, carbon atoms of various species function as acceptors of noncovalent interactions when they are part of a π-system. Here, we report on the discovery of a halogen bond involving the isocyano carbon lone pair. The co-crystallization or mechanochemical liquid-assisted grinding of model mesityl isocyanide w...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-16748-x

    authors： Mikherdov AS,Novikov AS,Boyarskiy VP,Kukushkin VY

    更新日期：2020-06-10 00:00:00

  • Sequence-regulated vinyl copolymers by metal-catalysed step-growth radical polymerization.

    abstract：:Proteins and nucleic acids are sequence-regulated macromolecules with various properties originating from their perfectly sequenced primary structures. However, the sequence regulation of synthetic polymers, particularly vinyl polymers, has not been achieved and is one of the ultimate goals in polymer chemistry. In th...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms1004

    authors： Satoh K,Ozawa S,Mizutani M,Nagai K,Kamigaito M

    更新日期：2010-04-12 00:00:00

  • Development of the macaque face-patch system.

    abstract：:Face recognition is highly proficient in humans and other social primates; it emerges in infancy, but the development of the neural mechanisms supporting this behaviour is largely unknown. We use blood-volume functional MRI to monitor longitudinally the responsiveness to faces, scrambled faces, and objects in macaque ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14897

    authors： Livingstone MS,Vincent JL,Arcaro MJ,Srihasam K,Schade PF,Savage T

    更新日期：2017-03-31 00:00:00

  • CHML promotes liver cancer metastasis by facilitating Rab14 recycle.

    abstract：:Metastasis-associated recurrence is the major cause of poor prognosis in hepatocellular carcinoma (HCC), however, the underlying mechanisms remain largely elusive. In this study, we report that expression of choroideremia-like (CHML) is increased in HCC, associated with poor survival, early recurrence and more satelli...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-10364-0

    authors： Chen TW,Yin FF,Yuan YM,Guan DX,Zhang E,Zhang FK,Jiang H,Ma N,Wang JJ,Ni QZ,Qiu L,Feng J,Zhang XL,Bao Y,Wang K,Cheng SQ,Wang XF,Wang X,Li JJ,Xie D

    更新日期：2019-06-07 00:00:00

  • A general-purpose machine-learning force field for bulk and nanostructured phosphorus.

    abstract：:Elemental phosphorus is attracting growing interest across fundamental and applied fields of research. However, atomistic simulations of phosphorus have remained an outstanding challenge. Here, we show that a universally applicable force field for phosphorus can be created by machine learning (ML) from a suitably chos...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-19168-z

    authors： Deringer VL,Caro MA,Csányi G

    更新日期：2020-10-29 00:00:00

  • Author Correction: Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR.

    abstract：:The original version of this Article contained an error in the author affiliations. Xiaochun Yu was incorrectly associated with College of Life Sciences, Hebei University, Baoding 071000 Hebei, China.This has now been corrected in both the PDF and HTML versions of the Article. ...

    journal_title：Nature communications

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41467-018-08086-w

    authors： Wang J,Yuan Z,Cui Y,Xie R,Yang G,Kassab MA,Wang M,Ma Y,Wu C,Yu X,Liu X

    更新日期：2019-01-08 00:00:00

  • Multi-omic data integration enables discovery of hidden biological regularities.

    abstract：:Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi-level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration of primary omics dat...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms13091

    authors： Ebrahim A,Brunk E,Tan J,O'Brien EJ,Kim D,Szubin R,Lerman JA,Lechner A,Sastry A,Bordbar A,Feist AM,Palsson BO

    更新日期：2016-10-26 00:00:00

  • Direct observation of ultrafast coherent exciton dynamics in helical π-stacks of self-assembled perylene bisimides.

    abstract：:Ever since the discovery of dye self-assemblies in nature, there have been tremendous efforts to exploit biomimetic supramolecular assemblies for tailored artificial photon processing materials. This feature necessarily has resulted in an increasing demand for understanding exciton dynamics in the dye self-assemblies....

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms9646

    authors： Sung J,Kim P,Fimmel B,Würthner F,Kim D

    更新日期：2015-10-23 00:00:00

  • A hepatic amino acid/mTOR/S6K-dependent signalling pathway modulates systemic lipid metabolism via neuronal signals.

    abstract：:Metabolism is coordinated among tissues and organs via neuronal signals. Levels of circulating amino acids (AAs), which are elevated in obesity, activate the intracellular target of rapamycin complex-1 (mTORC1)/S6kinase (S6K) pathway in the liver. Here we demonstrate that hepatic AA/mTORC1/S6K signalling modulates sys...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms8940

    authors： Uno K,Yamada T,Ishigaki Y,Imai J,Hasegawa Y,Sawada S,Kaneko K,Ono H,Asano T,Oka Y,Katagiri H

    更新日期：2015-08-13 00:00:00

  • Hour-glass magnetic excitations induced by nanoscopic phase separation in cobalt oxides.

    abstract：:The magnetic excitations in the cuprate superconductors might be essential for an understanding of high-temperature superconductivity. In these cuprate superconductors the magnetic excitation spectrum resembles an hour-glass and certain resonant magnetic excitations within are believed to be connected to the pairing m...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms6731

    authors： Drees Y,Li ZW,Ricci A,Rotter M,Schmidt W,Lamago D,Sobolev O,Rütt U,Gutowski O,Sprung M,Piovano A,Castellan JP,Komarek AC

    更新日期：2014-12-23 00:00:00

  • Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase.

    abstract：:Transcription in all living organisms is accomplished by multi-subunit RNA polymerases (msRNAPs). msRNAPs are highly conserved in evolution and invariably share a ∼400 kDa five-subunit catalytic core. Here we characterize a hypothetical ∼100 kDa single-chain protein, YonO, encoded by the SPβ prophage of Bacillus subti...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15774

    authors： Forrest D,James K,Yuzenkova Y,Zenkin N

    更新日期：2017-06-06 00:00:00

  • Merging of metal nanoparticles driven by selective wettability of silver nanostructures.

    abstract：:The welding and sintering of nanomaterials is relevant, for example, to form electrical contacts between metallic particles in printed electronic devices. Usually the welding of nanoparticles is achieved at high temperatures. Here we find that merging of two different metals, silver and gold nanoparticles, occurs on c...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3994

    authors： Grouchko M,Roitman P,Zhu X,Popov I,Kamyshny A,Su H,Magdassi S

    更新日期：2014-01-01 00:00:00