메뉴 건너뛰기




Volumn 6, Issue JUL, 2015, Pages

An introduction to automated flow cytometry gating tools and their implementation

Author keywords

Automated analysis; Flow cytometry; Gating; High throughput; Immunology; Software

Indexed keywords

ALGORITHM; ARTICLE; CELL POPULATION; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; FLOW CYTOMETRY; FLUORESCENCE; GATING; HUMAN; INFORMATION PROCESSING; LABORATORY AUTOMATION; MATHEMATICAL ANALYSIS;

EID: 84938511900     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2015.00380     Document Type: Article
Times cited : (65)

References (32)
  • 1
    • 84865592340 scopus 로고    scopus 로고
    • Cytometry: today's technology and tomorrow's horizons
    • Chattopadhyay PK, Roederer M. Cytometry: today's technology and tomorrow's horizons. Methods (2012) 57(3):251-8. doi: 10.1016/j.ymeth.2012.02.009
    • (2012) Methods , vol.57 , Issue.3 , pp. 251-258
    • Chattopadhyay, P.K.1    Roederer, M.2
  • 4
    • 84875658458 scopus 로고    scopus 로고
    • Blood CD33(+)HLA-DR(-) myeloid-derived suppressor cells are increased with age and a history of cancer
    • Verschoor CP, Johnstone J, Millar J, Dorrington MG, Habibagahi M, Lelic A, et al. Blood CD33(+)HLA-DR(-) myeloid-derived suppressor cells are increased with age and a history of cancer. J Leukoc Biol (2013) 93(4):633-7. doi:10.1189/jlb.0912461
    • (2013) J Leukoc Biol , vol.93 , Issue.4 , pp. 633-637
    • Verschoor, C.P.1    Johnstone, J.2    Millar, J.3    Dorrington, M.G.4    Habibagahi, M.5    Lelic, A.6
  • 5
    • 84905649973 scopus 로고    scopus 로고
    • Alterations to the frequency and function of peripheral blood monocytes and associations with chronic disease in the advanced-age, frail elderly
    • Verschoor CP, Johnstone J, Millar J, Parsons R, Lelic A, Loeb M, et al. Alterations to the frequency and function of peripheral blood monocytes and associations with chronic disease in the advanced-age, frail elderly. PLoS One (2014) 9(8):e104522. doi:10.1371/journal.pone.0104522
    • (2014) PLoS One , vol.9 , Issue.8
    • Verschoor, C.P.1    Johnstone, J.2    Millar, J.3    Parsons, R.4    Lelic, A.5    Loeb, M.6
  • 6
    • 84922213705 scopus 로고    scopus 로고
    • Circulating TNF and mitochondrial DNA are major determinants of neutrophil phenotype in the advanced-age, frail elderly
    • Verschoor CP, Loukov D, Naidoo A, Puchta A, Johnstone J, Millar J, et al. Circulating TNF and mitochondrial DNA are major determinants of neutrophil phenotype in the advanced-age, frail elderly. Mol Immunol (2015) 65(1):148-56. doi:10.1016/j.molimm.2015.01.015
    • (2015) Mol Immunol , vol.65 , Issue.1 , pp. 148-156
    • Verschoor, C.P.1    Loukov, D.2    Naidoo, A.3    Puchta, A.4    Johnstone, J.5    Millar, J.6
  • 7
    • 84907481710 scopus 로고    scopus 로고
    • Immune biomarkers predictive of respiratory viral infection in elderly nursing home residents
    • Johnstone J, Parsons R, Botelho F, Millar J, McNeil S, Fulop T, et al. Immune biomarkers predictive of respiratory viral infection in elderly nursing home residents. PLoS One (2014) 9(9):e108481. doi:10.1371/journal.pone.0108481
    • (2014) PLoS One , vol.9 , Issue.9
    • Johnstone, J.1    Parsons, R.2    Botelho, F.3    Millar, J.4    McNeil, S.5    Fulop, T.6
  • 9
    • 84856515333 scopus 로고    scopus 로고
    • Expansion of a CD8(+)PD-1(+) replicative senescence phenotype in early stage CLL patients is associated with inverted CD4:CD8 ratios and disease progression
    • Nunes C, Wong R, Mason M, Fegan C, Man S, Pepper C. Expansion of a CD8(+)PD-1(+) replicative senescence phenotype in early stage CLL patients is associated with inverted CD4:CD8 ratios and disease progression. Clin Cancer Res (2012) 18(3):678-87. doi:10.1158/1078-0432.CCR-11-2630
    • (2012) Clin Cancer Res , vol.18 , Issue.3 , pp. 678-687
    • Nunes, C.1    Wong, R.2    Mason, M.3    Fegan, C.4    Man, S.5    Pepper, C.6
  • 10
    • 58149103849 scopus 로고    scopus 로고
    • The presence of CD56/CD16 in T-cell acute lymphoblastic leukaemia correlates with the expression of cytotoxic molecules and is associated with worse response to treatment
    • Dalmazzo LFF, Jácomo RH, Marinato AF, Figueiredo-Pontes LL, Cunha RLG, Garcia AB, et al. The presence of CD56/CD16 in T-cell acute lymphoblastic leukaemia correlates with the expression of cytotoxic molecules and is associated with worse response to treatment. Br J Haematol (2009) 144(2):223-9. doi:10.1111/j.1365-2141.2008.07457.x
    • (2009) Br J Haematol , vol.144 , Issue.2 , pp. 223-229
    • Dalmazzo, L.F.F.1    Jácomo, R.H.2    Marinato, A.F.3    Figueiredo-Pontes, L.L.4    Cunha, R.L.G.5    Garcia, A.B.6
  • 11
    • 84874666550 scopus 로고    scopus 로고
    • Critical assessment of automated flow cytometry data analysis techniques
    • Aghaeepour N, Finak G; FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, et al. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods (2013) 10(3):228-38. doi:10.1038/nmeth.2365
    • (2013) Nat Methods , vol.10 , Issue.3 , pp. 228-238
    • Aghaeepour, N.1    Finak, G.2    Hoos, H.3    Mosmann, T.R.4
  • 12
    • 55949121648 scopus 로고    scopus 로고
    • Standardization and optimization of multiparameter intracellular cytokine staining
    • Nomura L, Maino VC, Maecker HT. Standardization and optimization of multiparameter intracellular cytokine staining. Cytometry A (2008) 73(11):984-91. doi:10.1002/cyto.a.20602
    • (2008) Cytometry A , vol.73 , Issue.11 , pp. 984-991
    • Nomura, L.1    Maino, V.C.2    Maecker, H.T.3
  • 13
    • 84879602126 scopus 로고    scopus 로고
    • Standardization of CD62P measurement: results of an international comparative study
    • Levin E, Serrano K, Devine DV; Biomedical Excellence for Safer Transfusion (BEST) Collaborative. Standardization of CD62P measurement: results of an international comparative study. Vox Sang (2013) 105(1):38-46. doi:10.1111/vox.12023
    • (2013) Vox Sang , vol.105 , Issue.1 , pp. 38-46
    • Levin, E.1    Serrano, K.2    Devine, D.V.3
  • 14
    • 84938414151 scopus 로고    scopus 로고
    • Data analysis as a source of variability of the HLA-peptide multimer assay: from manual gating to automated recognition of cell clusters
    • Gouttefangeas C, Chan C, Attig S, Køllgaard TT, Rammensee H-G, Stevanovic S, et al. Data analysis as a source of variability of the HLA-peptide multimer assay: from manual gating to automated recognition of cell clusters. Cancer Immunol Immunother (2015) 64(5):585-98. doi:10.1007/s00262-014-1649-1
    • (2015) Cancer Immunol Immunother , vol.64 , Issue.5 , pp. 585-598
    • Gouttefangeas, C.1    Chan, C.2    Attig, S.3    Køllgaard, T.T.4    Rammensee, H.-G.5    Stevanovic, S.6
  • 15
    • 84933509460 scopus 로고    scopus 로고
    • Automated flow cytometric analysis across large numbers of samples and cell types
    • Chen X, Hasan M, Libri V, Urrutia A, Beitz B, Rouilly V, et al. Automated flow cytometric analysis across large numbers of samples and cell types. Clin Immunol (2015) 157(2):249-60. doi:10.1016/j.clim.2014.12.009
    • (2015) Clin Immunol , vol.157 , Issue.2 , pp. 249-260
    • Chen, X.1    Hasan, M.2    Libri, V.3    Urrutia, A.4    Beitz, B.5    Rouilly, V.6
  • 16
    • 84925550970 scopus 로고    scopus 로고
    • Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm
    • Feher K, Kirsch J, Radbruch A, Chang H-D, Kaiser T. Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm. Bioinformatics (2014) 30(23):3372-8. doi:10.1093/bioinformatics/btu575
    • (2014) Bioinformatics , vol.30 , Issue.23 , pp. 3372-3378
    • Feher, K.1    Kirsch, J.2    Radbruch, A.3    Chang, H.-D.4    Kaiser, T.5
  • 17
    • 77949555869 scopus 로고    scopus 로고
    • Merging mixture components for cell population identification in flow cytometry
    • Finak G, Bashashati A, Brinkman R, Gottardo R. Merging mixture components for cell population identification in flow cytometry. Adv Bioinformatics (2009). doi:10.1155/2009/247646 Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798116/
    • (2009) Adv Bioinformatics
    • Finak, G.1    Bashashati, A.2    Brinkman, R.3    Gottardo, R.4
  • 18
    • 77954270805 scopus 로고    scopus 로고
    • A survey of flow cytometry data analysis methods
    • Bashashati A, Brinkman RR. A survey of flow cytometry data analysis methods. Adv Bioinformatics (2009):584603. doi:10.1155/2009/584603
    • (2009) Adv Bioinformatics
    • Bashashati, A.1    Brinkman, R.R.2
  • 19
    • 78650467489 scopus 로고    scopus 로고
    • On extensions of k-means clustering for automated gating of flow cytometry data
    • Luta G. On extensions of k-means clustering for automated gating of flow cytometry data. Cytometry A (2011) 79(1):3-5. doi:10.1002/cyto.a.20988
    • (2011) Cytometry A , vol.79 , Issue.1 , pp. 3-5
    • Luta, G.1
  • 20
    • 78650436333 scopus 로고    scopus 로고
    • Rapid cell population identification in flow cytometry data
    • Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR. Rapid cell population identification in flow cytometry data. Cytometry A (2011) 79(1):6-13. doi:10.1002/cyto.a.21007
    • (2011) Cytometry A , vol.79 , Issue.1 , pp. 6-13
    • Aghaeepour, N.1    Nikolic, R.2    Hoos, H.H.3    Brinkman, R.R.4
  • 22
    • 84865139571 scopus 로고    scopus 로고
    • flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
    • Ge Y, Sealfon SC. flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding. Bioinformatics (2012) 28(15):2052-8. doi:10.1093/bioinformatics/bts300
    • (2012) Bioinformatics , vol.28 , Issue.15 , pp. 2052-2058
    • Ge, Y.1    Sealfon, S.C.2
  • 23
  • 24
    • 80054768631 scopus 로고    scopus 로고
    • Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
    • Qiu P, Simonds EF, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, et al. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol (2011) 29(10):886-91. doi:10.1038/nbt.1991
    • (2011) Nat Biotechnol , vol.29 , Issue.10 , pp. 886-891
    • Qiu, P.1    Simonds, E.F.2    Bendall, S.C.3    Gibbs, K.D.4    Bruggner, R.V.5    Linderman, M.D.6
  • 25
    • 84928189767 scopus 로고    scopus 로고
    • flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification
    • Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR. flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. Bioinformatics (2015) 31(4):606-7. doi:10.1093/bioinformatics/btu677
    • (2015) Bioinformatics , vol.31 , Issue.4 , pp. 606-607
    • Malek, M.1    Taghiyar, M.J.2    Chong, L.3    Finak, G.4    Gottardo, R.5    Brinkman, R.R.6
  • 26
    • 84872040653 scopus 로고    scopus 로고
    • The polyfunctionality of human memory CD8+ T cells elicited by acute and chronic virus infections is not influenced by age
    • Lelic A, Verschoor CP, Ventresca M, Parsons R, Evelegh C, Bowdish D, et al. The polyfunctionality of human memory CD8+ T cells elicited by acute and chronic virus infections is not influenced by age. PLoS Pathog (2012) 8(12):e1003076. doi:10.1371/journal.ppat.1003076
    • (2012) PLoS Pathog , vol.8 , Issue.12
    • Lelic, A.1    Verschoor, C.P.2    Ventresca, M.3    Parsons, R.4    Evelegh, C.5    Bowdish, D.6
  • 27
    • 66649115648 scopus 로고    scopus 로고
    • Automated high-dimensional flow cytometric data analysis
    • Pyne S, Hu X, Wang K, Rossin E, Lin T-I, Maier LM, et al. Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci U S A (2009) 106(21):8519-24. doi:10.1073/pnas.0903028106
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.21 , pp. 8519-8524
    • Pyne, S.1    Hu, X.2    Wang, K.3    Rossin, E.4    Lin, T.-I.5    Maier, L.M.6
  • 28
    • 77956565464 scopus 로고    scopus 로고
    • Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data
    • Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, et al. Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin Cytom (2010) 78(Suppl 1):S69-82. doi:10.1002/cyto.b.20554
    • (2010) Cytometry B Clin Cytom , vol.78 , pp. S69-S82
    • Qian, Y.1    Wei, C.2    Eun-Hyung Lee, F.3    Campbell, J.4    Halliley, J.5    Lee, J.A.6
  • 29
    • 77954938186 scopus 로고    scopus 로고
    • Data reduction for spectral clustering to analyze high throughput flow cytometry data
    • Zare H, Shooshtari P, Gupta A, Brinkman RR. Data reduction for spectral clustering to analyze high throughput flow cytometry data. BMC Bioinformatics (2010) 11:403. doi:10.1186/1471-2105-11-403
    • (2010) BMC Bioinformatics , vol.11 , pp. 403
    • Zare, H.1    Shooshtari, P.2    Gupta, A.3    Brinkman, R.R.4
  • 30
    • 79952839584 scopus 로고    scopus 로고
    • TCLUST: a fast method for clustering genome-scale expression data
    • Dost B, Wu C, Su A, Bafna V. TCLUST: a fast method for clustering genome-scale expression data. IEEE/ACM Trans Comput Biol Bioinform (2011) 8(3):808-18. doi:10.1109/TCBB.2010.34
    • (2011) IEEE/ACM Trans Comput Biol Bioinform , vol.8 , Issue.3 , pp. 808-818
    • Dost, B.1    Wu, C.2    Su, A.3    Bafna, V.4
  • 31
    • 84961288133 scopus 로고    scopus 로고
    • OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis
    • Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, et al. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput Biol (2014) 10(8):e1003806. doi:10.1371/journal.pcbi.1003806
    • (2014) PLoS Comput Biol , vol.10 , Issue.8
    • Finak, G.1    Frelinger, J.2    Jiang, W.3    Newell, E.W.4    Ramey, J.5    Davis, M.M.6
  • 32
    • 84901459546 scopus 로고    scopus 로고
    • ImmPort: disseminating data to the public for the future of immunology
    • Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, et al. ImmPort: disseminating data to the public for the future of immunology. Immunol Res (2014) 58(2-3):234-9. doi:10.1007/s12026-014-8516-1
    • (2014) Immunol Res , vol.58 , Issue.2-3 , pp. 234-239
    • Bhattacharya, S.1    Andorf, S.2    Gomes, L.3    Dunn, P.4    Schaefer, H.5    Pontius, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.