Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE).

Abstract:

:Mass cytometry enables an unprecedented number of parameters to be measured in individual cells at a high throughput, but the large dimensionality of the resulting data severely limits approaches relying on manual "gating." Clustering cells based on phenotypic similarity comes at a loss of single-cell resolution and often the number of subpopulations is unknown a priori. Here we describe ACCENSE, a tool that combines nonlinear dimensionality reduction with density-based partitioning, and displays multivariate cellular phenotypes on a 2D plot. We apply ACCENSE to 35-parameter mass cytometry data from CD8(+) T cells derived from specific pathogen-free and germ-free mice, and stratify cells into phenotypic subpopulations. Our results show significant heterogeneity within the known CD8(+) T-cell subpopulations, and of particular note is that we find a large novel subpopulation in both specific pathogen-free and germ-free mice that has not been described previously. This subpopulation possesses a phenotypic signature that is distinct from conventional naive and memory subpopulations when analyzed by ACCENSE, but is not distinguishable on a biaxial plot of standard markers. We are able to automatically identify cellular subpopulations based on all proteins analyzed, thus aiding the full utilization of powerful new single-cell technologies such as mass cytometry.

authors

Shekhar K,Brodin P,Davis MM,Chakraborty AK

doi

10.1073/pnas.1321405111

subject

Has Abstract

pub_date

2014-01-07 00:00:00

pages

202-7

issue

1

eissn

0027-8424

issn

1091-6490

pii

1321405111

journal_volume

111

pub_type

杂志文章
  • Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center.

    abstract::3-(4'-Benzoylphenyl)propionyl[3H] Phe-tRNA bound to the peptidyl site of the ribosome is photo-crosslinked exclusively to 23S RNA on irradiation at 320 nm. The site of reaction has been identified both by hybridization and primer-extension experiments as uridine-2584 and uridine-2585, located within the central loop o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.12.3607

    authors: Barta A,Steiner G,Brosius J,Noller HF,Kuechler E

    更新日期:1984-06-01 00:00:00

  • Sulfated glycosaminoglycans mediate prion-like behavior of p53 aggregates.

    abstract::Sulfated glycosaminoglycans (GAGs) such as heparan sulfate (HS) are heteropolysaccharides implicated in the pathology of protein aggregation diseases including localized and systemic forms of amyloidosis. Among subdomains of sulfated GAGs, highly sulfated domains of HS, called HS S-domains, have been highlighted as be...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2009931117

    authors: Iwahashi N,Ikezaki M,Nishikawa T,Namba N,Ohgita T,Saito H,Ihara Y,Shimanouchi T,Ino K,Uchimura K,Nishitsuji K

    更新日期:2020-12-29 00:00:00

  • Higher-order syzygies for the bracket algebra and for the ring of coordinates of the Grassmanian.

    abstract::A Poincaré resolution is given for the supersymmetric ring of brackets over a signed alphabet. As a consequence, a resolution is found for the ring of coordinates of the Grassmanian variety in projective space over any infinite field. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.18.8087

    authors: Anick D,Rota GC

    更新日期:1991-09-15 00:00:00

  • Physical and functional interactions between Drosophila TRAF2 and Pelle kinase contribute to Dorsal activation.

    abstract::Signaling through the Toll receptor is required for dorsal/ventral polarity in Drosophila embryos, and also plays an evolutionarily conserved role in the immune response. Upon ligand binding, Toll appears to multimerize and activate the associated kinase, Pelle. However, the immediate downstream targets of Pelle have ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.141235698

    authors: Shen B,Liu H,Skolnik EY,Manley JL

    更新日期:2001-07-17 00:00:00

  • Particles containing RNA-instructed DNA polymerase and virus-related RNA in human breast cancers.

    abstract::Human breast cancers contain an RNA related to that of mouse mammary tumor virus. In 79% of the breast malignancies examined, this type of RNA is a 70S-component encapsulated with RNA-instructed DNA polymerase in a particle possessing the density characteristics of RNA tumor viruses. Further, the DNA synthesized by th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.69.11.3133

    authors: Axel R,Gulati SC,Spiegelman S

    更新日期:1972-11-01 00:00:00

  • Versatile selection technology for intracellular protein-protein interactions mediated by a unique bacterial hitchhiker transport mechanism.

    abstract::We have developed a reliable genetic selection strategy for isolating interacting proteins based on the "hitchhiker" mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway. This method, designated FLI-TRAP (functional ligand-binding identification by Tat-based recognition of associating proteins),...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0704048106

    authors: Waraho D,DeLisa MP

    更新日期:2009-03-10 00:00:00

  • Molecular basis for heterosis for myelin basic protein content in mice.

    abstract::Poly(A)+ mRNA was isolated from the brains of C57BL/6J (B6), DBA/2J (D2), and F1 hybrid mice (B6 X D2) of 16-17 days of age. The yield of polysomal RNA, both poly(A)+ and poly(A)-, from the three strains of mice was comparable. When translated in vitro in a reticulocyte lysate system, the mRNA preparations had the sam...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.5.1532

    authors: Miskimins R,Ebato H,Seyfried TN,Yu RK

    更新日期:1986-03-01 00:00:00

  • White lines in L-edge x-ray absorption spectra and their implications for anomalous diffraction studies of biological materials.

    abstract::We have measured high-resolution x-ray absorption spectra of lanthanide (Ln) and heavy transition metal complexes that display prominent narrow absorption peaks near the L2 and L3 absorption edges. The anomalous scattering factors (f' and f"), which are mathematically related to the absorption cross section, have corr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.10.5884

    authors: Lye RC,Phillips JC,Kaplan D,Doniach S,Hodgson KO

    更新日期:1980-10-01 00:00:00

  • Sequences near the termini are required for transposition of the maize transposon Ac in transgenic tobacco plants.

    abstract::Deletion derivatives of the maize transposable element Activator (Ac) were constructed in vitro and inserted into a kanamycin resistance gene. These constructions were then introduced into tobacco protoplasts derived from plants previously transformed with Ac. The ability of each deletion derivative to excise was meas...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.23.9385

    authors: Coupland G,Plum C,Chatterjee S,Post A,Starlinger P

    更新日期:1989-12-01 00:00:00

  • Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins.

    abstract::Extracellular growth and differentiation factors induce changes in gene expression in the nucleus by initiating a series of protein associations that alter the subcellular localization of intracellular signaling proteins. Initial events involve receptor homo- or heterodimerization and subsequent recruitment of cytosol...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.10.4604

    authors: Belshaw PJ,Ho SN,Crabtree GR,Schreiber SL

    更新日期:1996-05-14 00:00:00

  • Exosome-mediated transmission of hepatitis C virus between human hepatoma Huh7.5 cells.

    abstract::Recent evidence indicates there is a role for small membrane vesicles, including exosomes, as vehicles for intercellular communication. Exosomes secreted by most cell types can mediate transfer of proteins, mRNAs, and microRNAs, but their role in the transmission of infectious agents is less established. Recent studie...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1221899110

    authors: Ramakrishnaiah V,Thumann C,Fofana I,Habersetzer F,Pan Q,de Ruiter PE,Willemsen R,Demmers JA,Stalin Raj V,Jenster G,Kwekkeboom J,Tilanus HW,Haagmans BL,Baumert TF,van der Laan LJ

    更新日期:2013-08-06 00:00:00

  • Regulation of binding properties of the nicotinic receptor protein by cholinergic ligands in membrane fragments from Torpedo marmorata.

    abstract::Exposure of receptor-rich membrane fragments from Torpedo marmorata to carbamylcholine causes a slow (half-time of 5--10 min) and reversible change of properties of the cholinergic receptor protein manifested by a decrease of the initial rate of Naja nigricollis alpha-[3H]toxin binding in the presence of carbamylcholi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.72.9.3443

    authors: Weber M,David-Pfeuty T,Changeux JP

    更新日期:1975-09-01 00:00:00

  • Speech-like cerebral activity in profoundly deaf people processing signed languages: implications for the neural basis of human language.

    abstract::For more than a century we have understood that our brain's left hemisphere is the primary site for processing language, yet why this is so has remained more elusive. Using positron emission tomography, we report cerebral blood flow activity in profoundly deaf signers processing specific aspects of sign language in ke...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.25.13961

    authors: Petitto LA,Zatorre RJ,Gauna K,Nikelski EJ,Dostie D,Evans AC

    更新日期:2000-12-05 00:00:00

  • The identification of Hoxc8 target genes.

    abstract::Hox genes encode transcription factors that control spatial patterning during embryogenesis. To date, downstream targets of Hox genes have proven difficult to identify. Here, we describe studies designed to identify target genes under the control of the murine transcription factor Hoxc8. We used a mouse 16,463 gene ol...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0409700102

    authors: Lei H,Wang H,Juan AH,Ruddle FH

    更新日期:2005-02-15 00:00:00

  • Room-temperature single-electron junction.

    abstract::The design, realization, and test performances of an electronic junction based on single-electron phenomena that works in the air at room temperature are hereby reported. The element consists of an electrochemically etched sharp tungsten stylus over whose tip a nanometer-size crystal was synthesized. Langmuir-Blodgett...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.20.10556

    authors: Facci P,Erokhin V,Carrara S,Nicolini C

    更新日期:1996-10-01 00:00:00

  • Fidelity of adaptive phototaxis.

    abstract::Along the evolutionary path from single cells to multicellular organisms with a central nervous system are species of intermediate complexity that move in ways suggesting high-level coordination, yet have none. Instead, organisms of this type possess many autonomous cells endowed with programs that have evolved to ach...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1000901107

    authors: Drescher K,Goldstein RE,Tuval I

    更新日期:2010-06-22 00:00:00

  • Enantiomer excesses of rare and common sugar derivatives in carbonaceous meteorites.

    abstract::Biological polymers such as nucleic acids and proteins are constructed of only one-the d or l-of the two possible nonsuperimposable mirror images (enantiomers) of selected organic compounds. However, before the advent of life, it is generally assumed that chemical reactions produced 50:50 (racemic) mixtures of enantio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1603030113

    authors: Cooper G,Rios AC

    更新日期:2016-06-14 00:00:00

  • Distinct forms of cholinergic modulation in parallel thalamic sensory pathways.

    abstract::Mammalian thalamus is a critical site where early perception of sensorimotor signals is dynamically regulated by acetylcholine in a behavioral state-dependent manner. In this study, we examined how synaptic transmission is modulated by acetylcholine in auditory thalamus where sensory relay neurons form parallel lemnis...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0304445101

    authors: Mooney DM,Zhang L,Basile C,Senatorov VV,Ngsee J,Omar A,Hu B

    更新日期:2004-01-06 00:00:00

  • Modulation of epidermal growth factor receptors by human alpha interferon.

    abstract::Treatment of Madin-Darby bovine kidney (MDBK) cells with human interferon (IFN)-alpha 2 at 37 degrees C results in a dose-dependent inhibition of cell growth and a reduction of the subsequent binding of 125I-labeled epidermal growth factor (EGF) at 4 degrees C. Human IFN-beta and -gamma, which exhibit little antiviral...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.21.8226

    authors: Zoon KC,Karasaki Y,zur Nedden DL,Hu RQ,Arnheiter H

    更新日期:1986-11-01 00:00:00

  • Oxygen isotopes in tree rings are a good proxy for Amazon precipitation and El Nino-Southern Oscillation variability.

    abstract::We present a unique proxy for the reconstruction of variation in precipitation over the Amazon: oxygen isotope ratios in annual rings in tropical cedar (Cedrela odorata). A century-long record from northern Bolivia shows that tree rings preserve the signal of oxygen isotopes in precipitation during the wet season, wit...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1205977109

    authors: Brienen RJ,Helle G,Pons TL,Guyot JL,Gloor M

    更新日期:2012-10-16 00:00:00

  • On the primary nature of fluorescence yield changes associated with photosynthesis.

    abstract::Absorbance changes of C-550 and cytochrome b(559), and fluorescence-yield changes were measured during irradiation of chloroplasts at -196 degrees . The photo-reduction of C-550 proceeded more rapidly than the photo-oxidation of cytochrome b(559), and the fluorescence-yield change had similar kinetics to the cytochrom...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.69.11.3420

    authors: Butler WL

    更新日期:1972-11-01 00:00:00

  • Pex1, a pollen-specific gene with an extensin-like domain.

    abstract::We report here the identification of a pollen-specific gene from Zea mays that contains multiple Ser-(Pro)n repeats, the motif found in the cell wall-associated extensins. Sequence analysis reveals that the encoded protein has a putative globular domain at the N terminus and an extensin-like domain at the C terminus. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.8.3086

    authors: Rubinstein AL,Broadwater AH,Lowrey KB,Bedinger PA

    更新日期:1995-04-11 00:00:00

  • Quality-control mechanisms targeting translationally stalled and C-terminally extended poly(GR) associated with ALS/FTD.

    abstract::Maintaining the fidelity of nascent peptide chain (NP) synthesis is essential for proteome integrity and cellular health. Ribosome-associated quality control (RQC) serves to resolve stalled translation, during which untemplated Ala/Thr residues are added C terminally to stalled peptide, as shown during C-terminal Ala ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2005506117

    authors: Li S,Wu Z,Tantray I,Li Y,Chen S,Dong J,Glynn S,Vogel H,Snyder M,Lu B

    更新日期:2020-10-06 00:00:00

  • A gene atlas of the mouse and human protein-encoding transcriptomes.

    abstract::The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of pr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0400782101

    authors: Su AI,Wiltshire T,Batalov S,Lapp H,Ching KA,Block D,Zhang J,Soden R,Hayakawa M,Kreiman G,Cooke MP,Walker JR,Hogenesch JB

    更新日期:2004-04-20 00:00:00

  • Adeno-associated virus type-2 expression of pigmented epithelium-derived factor or Kringles 1-3 of angiostatin reduce retinal neovascularization.

    abstract::Neovascular diseases of the retina include age-related macular degeneration and diabetic retinopathy, and together they comprise the leading causes of adult-onset blindness in developed countries. Current surgical, pharmaceutical, and laser therapies for age-related macular degeneration (AMD) rarely result in improved...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.122247299

    authors: Raisler BJ,Berns KI,Grant MB,Beliaev D,Hauswirth WW

    更新日期:2002-06-25 00:00:00

  • Isolation of an ovine pulmonary surfactant-associated anionic peptide bactericidal for Pasteurella haemolytica.

    abstract::Ovine pulmonary surfactant is bactericidal for Pasteurella haemolytica when surfactant and bacteria mixtures are incubated with normal ovine serum. To isolate this component, surfactant (1 mg/ml) was centrifuged at 100,000 x gav, and the supernatant was fractionated by HPLC. Fractions were eluted with acetonitrile (10...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.1.412

    authors: Brogden KA,De Lucca AJ,Bland J,Elliott S

    更新日期:1996-01-09 00:00:00

  • Generation of dopaminergic neurons and pigmented epithelia from primate ES cells by stromal cell-derived inducing activity.

    abstract::We previously identified a stromal cell-derived inducing activity (SDIA), which induces differentiation of neural cells, including midbrain tyrosine hydroxylase-positive (TH(+)) dopaminergic neurons, from mouse embryonic stem cells. We report here that SDIA induces efficient neural differentiation also in primate embr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.032662199

    authors: Kawasaki H,Suemori H,Mizuseki K,Watanabe K,Urano F,Ichinose H,Haruta M,Takahashi M,Yoshikawa K,Nishikawa S,Nakatsuji N,Sasai Y

    更新日期:2002-02-05 00:00:00

  • Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli.

    abstract::A strain of Escherichia coli, selected on the basis of its resistance to colicin N, reveals distinct structural and functional alterations in unspecific OmpF porin. A single mutation [Gly-119-->Asp (G119D)] was identified in the internal loop L3 that contributes critically to the formation of the construction inside t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.22.10675

    authors: Jeanteur D,Schirmer T,Fourel D,Simonet V,Rummel G,Widmer C,Rosenbusch JP,Pattus F,Pagès JM

    更新日期:1994-10-25 00:00:00

  • Structure of the lambda att sites generated by int-dependent deletions.

    abstract::Bacteriophage lambda integrates into the chromosome of its Escherichia coli host by means of a site-specific recombination between a locus on the phage chromosome (phage att site) and a locus on the bacterial chromosome (bacterial att site). The nucleotide sequence of four lambda att sites altered in site-specific rec...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.75.11.5437

    authors: Hoess RH,Landy A

    更新日期:1978-11-01 00:00:00

  • An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.

    abstract::The nucleotide cyclic di-3',5'- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP-producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular un...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1416485112

    authors: Huynh TN,Luo S,Pensinger D,Sauer JD,Tong L,Woodward JJ

    更新日期:2015-02-17 00:00:00