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1.
BMC Biol ; 19(1): 5, 2021 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-33441133

RESUMO

BACKGROUND: Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. RESULTS: We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28-34%, genus level). PHP also outperformed these two alignment-free methods much (24-38% vs 18-20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. CONCLUSIONS: The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

2.
Cell Res ; 2021 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-33510385

RESUMO

The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 genomic RNA, as well as the negative-sense RNA, is dynamically N6-methyladenosine (m6A)-modified in human and monkey cells. Combined RIP-seq and miCLIP analyses identified a total of 8 m6A sites at single-base resolution in the genome. Especially, epidemic strains with mutations at these identified m6A sites have emerged worldwide, and formed a unique cluster in the US as indicated by phylogenetic analysis. Further functional experiments showed that m6A methylation negatively regulates SARS-CoV-2 infection. SARS-CoV-2 infection also triggered a global increase in host m6A methylome, exhibiting altered localization and motifs of m6A methylation in mRNAs. Altogether, our results identify m6A as a dynamic epitranscriptomic mark mediating the virus-host interaction.

3.
Brief Bioinform ; 2021 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-33401306

RESUMO

Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.

4.
Waste Manag ; 2020 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-33281044

RESUMO

Waste electrical and electronic equipment (viz., WEEE or e-waste) is the fastest-growing type of hazardous solid waste in the worldwide. The accurate prediction of the amount of e-waste might help improve the efficiency of e-waste disposal. In this study, a novel decomposition-ensemble-based hybrid forecasting methodology that integrates variational mode decomposition (VMD), exponential smoothing model (ESM), and grey modeling (GM) methods (named VMD-ESM-GM) is proposed for e-waste quantity prediction. For verification purposes, sample data from Washington State, US, and UK Environment Agency are analyzed. Compared to benchmark models, the proposed VMD-ESM-GM methodology not only obtains a satisfactory prediction result for e-waste data but also predicts the future fluctuation trend of e-waste. These results indicate that the proposed VMD-ESM-GM methodology based on the decomposition-ensemble principle is a suitable model for the prediction of the e-waste quantity and could help decision-makers develop both e-waste recycling plans and circular economy plans.

5.
Artigo em Inglês | MEDLINE | ID: mdl-33331671

RESUMO

Herein, we present a new strategy for the synthesis of 2D porous MoP/Mo2 N heterojunction nanosheets based on the pyrolysis of 2D [PMo12 O40 ]3- -melamine (PMo12 -MA) nanosheet precursor from a polyethylene glycol (PEG)-mediated assembly route. The heterostructure nanosheets are ca. 20 nm thick and have plentiful pores (<5 nm). These structure features offer advantages to promote the HER activity, including the favorable water dissociation kinetics around heterojunction as confirmed by theoretical calculations, large accessible surface of 2D nanosheets, and enhanced mass-transport ability by pores. Consequently, the 2D porous MoP/Mo2 N heterojunction nanosheets exhibit excellent HER activity with low overpotentials of 89, 91 and 89 mV to achieve a current density of 10 mA cm-2 in alkaline, neutral and acidic electrolytes, respectively. The HER performance is superior to the commercial Pt/C at a current density >55 mA cm-2 in neutral medium and >190 mA cm-2 in alkaline medium.

6.
Brief Bioinform ; 2020 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-33313676

RESUMO

The genus Culicoides includes biting midges, some of which are vectors for viruses that cause diseases in humans and animals. Knowledge of the roles of Culicoides in viral ecology is inadequate. We collected ~300 000 samples of Culicoides and mosquitoes in 15 representative regions within Yunnan, China. Using mosquitoes as reference vectors, we designed a comparative virome strategy to study the viral composition, diversity, hosts and spatiotemporal distribution of Culicoides. A map of viromes in Culicoides and mosquitoes in Yunan province, China, was constructed. At the same locations, Culicoides and mosquitoes usually share a similar viral diversity. At least 10 important pathogenic viruses were detected from Culicoides. Many novel viruses were discovered, including 21 segmented viruses of Flaviviridae, 180 viruses of Monjiviricetes and 130 viruses of Bunyavirales. The findings demonstrate that Culicoides is an important part of viral ecology and should be studied and monitored for potentially emerging viruses.

7.
Brief Bioinform ; 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-33126244

RESUMO

Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1-10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.

8.
ACS Appl Mater Interfaces ; 12(44): 49596-49606, 2020 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-33089984

RESUMO

Molybdenum phosphide is one of the most potential electrocatalysts for the hydrogen evolution reaction (HER), whereas it is still challenging to achieve an efficient molybdenum phosphide-based catalyst that performs well over a wide pH range. Herein, a porous nanoplate composed of small MoP flakes confined in thin N, P, S-triple-doped carbon (MoP@NPSC) was prepared by the assembly of phosphomolybdic acid (H3PMo12O40·nH2O, {PMo12}) and egg white, followed by phosphorization. Given its small size (ca. 1 nm) in favor of deriving small particles and the oxygen-rich surface with strong coordination ability, the {PMo12} cluster was selected to combine with egg white to obtain a lamellar hybrid precursor via a hydrogen bond. Through controllable phosphating, a nanoplate organized by interconnected MoP particles was generated, accompanied by the in situ formation of the N, P, S-doped carbon thin layer and pores from the pyrolysis of egg white. The plentiful pores, thin carbon coating, and multielement doping bring about promoted electrolyte/bubble diffusion, enhanced conductivity and stability, and lowered adsorption energy of hydrogen/hydroxyl, respectively. All of the above merits endow MoP@NPSC with prominent activity with low overpotentials of 50, 76, and 71 mV at 10 mA cm-2 toward the HER in alkaline, neutral, and acid media, respectively, and nearly no attenuation after 40 h of testing. Especially, compared with commercial Pt/C, MoP@NPSC exhibits similar low onset potential and even better at large current density in 1 M KOH. The electrolyzer equipped with the MoP@NPSC cathode and the NiFe-LDH anode requires only 1.52 V to deliver 10 mA cm-2 and can be powered by a solar cell (1.524 V) charged by sunlight.

9.
J Comp Eff Res ; 9(15): 1079-1090, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32959666

RESUMO

Aim: To assess the impact of oxidized regenerated cellulose (ORC) on blood transfusion and hospital costs associated with surgeries. Patients & methods: This retrospective cohort study selected ten surgeries to create propensity-score matching groups to compare ORC versus nonORC (conventional hemostatic techniques such as manual pressure, ligature and electrocautery). Results: NonORC was associated with both higher blood transfusion volume and higher hospital costs than ORC in endoscopic transnasal sphenoidal surgery, nonskull base craniotomy, hepatectomy, cholangiotomy, gastrectomy and lumbar surgery. However, nonORC was associated with better outcomes than ORC in open colorectal surgery, mammectomy and hip arthroplasty surgery. Conclusion: When compared with conventional hemostatic technique, using ORC could impact blood transfusion and hospital costs differently by surgical settings.

10.
Virol Sin ; 2020 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-32725480

RESUMO

The virus receptors are key for the viral infection of host cells. Identification of the virus receptors is still challenging at present. Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level, high number of interaction partners and high expression level. Here, a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences. A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome. In addition, the combination of the random-forest model with protein-protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses, such as the enterovirus, norovirus and West Nile virus. Finally, the candidate alternative receptors of the SARS-CoV-2 were also predicted in this study. As far as we know, this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.

11.
bioRxiv ; 2020 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-32511312

RESUMO

Background: The 2019 novel coronavirus (2019-nCoV or SARS-CoV-2) has spread more rapidly than any other betacoronavirus including SARS-CoV and MERS-CoV. However, the mechanisms responsible for infection and molecular evolution of this virus remained unclear. Methods: We collected and analyzed 120 genomic sequences of 2019-nCoV including 11 novel genomes from patients in China. Through comprehensive analysis of the available genome sequences of 2019-nCoV strains, we have tracked multiple inheritable SNPs and determined the evolution of 2019-nCoV relative to other coronaviruses. Results: Systematic analysis of 120 genomic sequences of 2019-nCoV revealed co-circulation of two genetic subgroups with distinct SNPs markers, which can be used to trace the 2019-nCoV spreading pathways to different regions and countries. Although 2019-nCoV, human and bat SARS-CoV share high homologous in overall genome structures, they evolved into two distinct groups with different receptor entry specificities through potential recombination in the receptor binding regions. In addition, 2019-nCoV has a unique four amino acid insertion between S1 and S2 domains of the spike protein, which created a potential furin or TMPRSS2 cleavage site. Conclusions: Our studies provided comprehensive insights into the evolution and spread of the 2019-nCoV. Our results provided evidence suggesting that 2019-nCoV may increase its infectivity through the receptor binding domain recombination and a cleavage site insertion. One Sentence Summary: Novel 2019-nCoV sequences revealed the evolution and specificity of betacoronavirus with possible mechanisms of enhanced infectivity.

12.
Adv Mater ; 32(17): e2000455, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32173914

RESUMO

Simultaneous highly efficient production of hydrogen and conversion of biomass into value-added products is meaningful but challenging. Herein, a porous nanospindle composed of carbon-encapsulated MoO2 -FeP heterojunction (MoO2 -FeP@C) is proposed as a robust bifunctional electrocatalyst for hydrogen evolution reaction (HER) and biomass electrooxidation reaction (BEOR). X-ray photoelectron spectroscopy analysis and theoretical calculations confirm the electron transfer from MoO2 to FeP at the interfaces, where electron accumulation on FeP favors the optimization of H2 O and H* absorption energies for HER, whereas hole accumulation on MoO2 is responsible for improving the BEOR activity. Thanks to its interfacial electronic structure, MoO2 -FeP@C exhibits excellent HER activity with an overpotential of 103 mV at 10 mA cm-2 and a Tafel slope of 48 mV dec-1 . Meanwhile, when 5-hydroxymethylfurfural is chosen as the biomass for BEOR, the conversion is almost 100%, and 2,5-furandicarboxylic acid (FDCA) is obtained with the selectivity of 98.6%. The electrolyzer employing MoO2 -FeP@C for cathodic H2 and anodic FDCA production requires only a low voltage of 1.486 V at 10 mA cm-2 and can be powered by a solar cell (output voltage: 1.45 V). Additionally, other BEORs coupled with HER catalyzed by MoO2 -FeP@C also have excellent catalytic performance, implying their good versatility.

13.
Bioinformatics ; 36(10): 3251-3253, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32049310

RESUMO

MOTIVATION: Newly emerging influenza viruses keep challenging global public health. To evaluate the potential risk of the viruses, it is critical to rapidly determine the phenotypes of the viruses, including the antigenicity, host, virulence and drug resistance. RESULTS: Here, we built FluPhenotype, a one-stop platform to rapidly determinate the phenotypes of the influenza A viruses. The input of FluPhenotype is the complete or partial genomic/protein sequences of the influenza A viruses. The output presents five types of information about the viruses: (i) sequence annotation including the gene and protein names as well as the open reading frames, (ii) potential hosts and human-adaptation-associated amino acid markers, (iii) antigenic and genetic relationships with the vaccine strains of different HA subtypes, (iv) mammalian virulence-related amino acid markers and (v) drug resistance-related amino acid markers. FluPhenotype will be a useful bioinformatic tool for surveillance and early warnings of the newly emerging influenza A viruses. AVAILABILITY AND IMPLEMENTATION: It is publicly available from: http://www.computationalbiology.cn : 18888/IVEW. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Vírus da Influenza A , Influenza Humana , Orthomyxoviridae , Sequência de Aminoácidos , Animais , Glicoproteínas de Hemaglutininação de Vírus da Influenza , Humanos , Vírus da Influenza A/genética
14.
Cell Host Microbe ; 27(3): 325-328, 2020 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-32035028

RESUMO

An in-depth annotation of the newly discovered coronavirus (2019-nCoV) genome has revealed differences between 2019-nCoV and severe acute respiratory syndrome (SARS) or SARS-like coronaviruses. A systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may have caused functional and pathogenic divergence of 2019-nCoV.


Assuntos
Betacoronavirus/classificação , Infecções por Coronavirus/virologia , Genoma Viral , Filogenia , Pneumonia Viral/virologia , Substituição de Aminoácidos , China , Coronavírus da Síndrome Respiratória do Oriente Médio , Pandemias , Vírus da SARS
15.
Chem Commun (Camb) ; 56(19): 2913-2916, 2020 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-32037411

RESUMO

An effective "precursor-transformation" route was developed for the high-yield synthesis of ZIF-8 tubes based on the reaction of 1D Zn-EG (ethylene glycol) wires with 2-methylimidazole (with around 0.6 g of ZIF-8/60 mL of solvent, the yield is over 90% based on Zn). The ZIF-8 tubes fixed on a sponge can be used as an effective material for oil/water separation.

16.
Bioinformatics ; 36(10): 2975-2979, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32096819

RESUMO

MOTIVATION: Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown. RESULTS: Here, we manually curated a high-quality database named phageReceptor, including 427 pairs of phage-host receptor interactions, 341 unique viral species or sub-species and 69 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The phage protein receptors (PPRs) were highly diverse in their structures, and had little sequence identity and no common protein domain with mammalian virus receptors. Further functional characterization of PPRs in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors reported in previous studies, suggesting that viral protein receptors tend to have multiple interaction partners and high expressions. The study deepens our understanding of virus-host interactions. AVAILABILITY AND IMPLEMENTATION: phageReceptor is publicly available from: http://www.computationalbiology.cn/phageReceptor/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Bacteriófagos , Receptores Virais , Animais , Bacteriófagos/genética , Escherichia coli , Proteínas de Membrana , Proteínas Virais
17.
Chemosphere ; 250: 126246, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32097811

RESUMO

A piscicide, rotenone (RT), is frequently used for clear and management of aquatic systems such as fish pond, and even for illegal fishing throughout the world. The effects of RT on submerged macrophytes remain elusive although the effects of RT on many kinds of animals are well documented. We wanted to determine the effects of RT on the growth and metabolism of three submerged plants (Vallisneria natans, Myriophyllum spicatum, Potamogeton maackianus) and try to find the reasons of these effects. The results showed that the shoot height, shoot dry weight, root dry weight, root:shoot ratios, contents of soluble protein and soluble carbohydrate of the three tested submerged plants were significantly negatively affected by RT and the effects were different among the studied species. Furthermore, pH rised a little and light transmission was greatly reduced in the water with RT treatment. We think that the negative effects of RT on the growth and metabolism of submerged species is partially attributing to the lower light caused by RT application. Accordingly, we highlight that submerged species may be greatly suppressed by RT, and we should apply RT in water ecosystems with great caution.


Assuntos
Hydrocharitaceae/efeitos dos fármacos , Praguicidas/toxicidade , Potamogetonaceae/efeitos dos fármacos , Rotenona/toxicidade , Ecossistema , Hydrocharitaceae/crescimento & desenvolvimento , Hydrocharitaceae/metabolismo , Potamogetonaceae/crescimento & desenvolvimento , Água/metabolismo
18.
J Invest Dermatol ; 140(9): 1824-1836.e7, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32092350

RESUMO

Langhans multinucleated giant cells (LGCs) are a specific type of multinucleated giant cell containing a characteristic horseshoe-shaped ring of nuclei that are present within granulomas of infectious etiology. Although cytokines that trigger macrophage activation (such as IFN-γ) induce LGC formation, it is not clear whether cytokines that trigger macrophage differentiation contribute to LGC formation. Here, we found that IL-15, a cytokine that induces M1 macrophage differentiation, programs human peripheral blood adherent cells to form LGCs. Analysis of the IL-15‒treated adherent cell transcriptome identified gene networks for T cells, DNA damage and replication, and IFN-inducible genes that correlated with IL-15 treatment and LGC-type multinucleated giant cell formation. Gene networks enriched for myeloid cells were anticorrelated with IL-15 treatment and LGC formation. Functional studies revealed that T cells were required for IL-15‒induced LGC formation, involving a direct contact with myeloid cells through CD40L-CD40 interaction and IFN-γ release. These data indicate that IL-15 induces LGC formation through the direct interaction of activated T cells and myeloid cells.

19.
JPEN J Parenter Enteral Nutr ; 44(5): 855-865, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-31429970

RESUMO

BACKGROUND: The 2012 European Society of Intensive Care Medicine (ESICM) guidelines provided a clear definition of feeding intolerance (FI). The study aimed to investigate the association between FI based on the current ESICM definition and clinical outcome and to further explore the effect of the duration of FI on mortality. METHODS: Adult patients from 14 general intensive care units (ICUs) with an expected ICU stay ≥24 hours were prospectively studied. Based on FI duration in the first week of admission to the ICU, FI was categorized as 7-day persistent feeding tolerance (FT), delayed FT, delayed FI, and 7-day persistent FI. The primary outcomes were 28-day and 60-day all-cause mortality. RESULTS: Of 499 patients, the prevalence of 3-day and 7-day persistent FI was 39.2% (n = 196) and 25.4% (n = 106), respectively. The patients with 3-day FT had lower risk of 28-day and 60-day mortality rates and higher prevalence in ventilator weaning and vasoactive medication on the seventh day of ICU admission than those with 3-day FI. Three-day FI remained an independent predictor for 60-day mortality. In a subgroup analysis including 418 patients with 7-day survival, compared with those with 7-day persistent FT, the odds ratios of 60-day mortality were 1.67, 1.97, and 2.62 in the patients with delayed FT, delayed FI, and 7-day persistent FI, respectively. CONCLUSION: FI was associated with increased mortality and longer duration of mechanical ventilation and vasoactive support. Prolonged or relapsing FI represented an incremental risk of adverse outcomes in critically ill patients.

20.
Bioinformatics ; 36(3): 819-827, 2020 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504185

RESUMO

MOTIVATION: Many methods have been developed to estimate immune cell composition from tissue transcriptomes. One common characteristic of these methods is that they are trained using a set of general immune cell transcriptomes that ignores tissue specificities. However, as immune cells are localized in different tissues, they may have distinct expression profiles. Hence, calculations that use general signature matrices may hinder the deconvolution accuracy. RESULTS: This study used single cell RNA-sequencing (scRNA-Seq) data from different mouse tissues instead of general signature expression values to generate tissue-specific signature gene matrices that are used as the input of the deconvolution model. First, the transcriptome of immune cells in each tissue was extracted from scRNA-Seq data and used to construct the entire expression matrix of tissue immune cells. Then, after comparing different gene selection strategies, the expressions of 162 seq-ImmuCC derived signature genes in tissue immune cell scRNA-Seq data were regarded as the tissue specific signature matrices. Finally, a modest improvement in performance was observed in multiple tissues that refer to a traditional general signature matrix in the deconvolution model. With the fast accumulation of scRNA-Seq data, the introduction of these data into an estimation of immune cell compositions for different tissues will open a new window for avoiding tissue bias for immune cell expression. AVAILABILITY AND IMPLEMENTATION: The signature matrices were available at https://github.com/wuaipinglab/ImmuCC/tree/master/tissue_immucc/SignatureMatrix). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Perfilação da Expressão Gênica , Transcriptoma , Animais , Sequência de Bases , Camundongos , Análise de Sequência de RNA , Análise de Célula Única
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