메뉴 건너뛰기




Volumn 18, Issue 1, 2017, Pages

xCell: Digitally portraying the tissue cellular heterogeneity landscape

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL HETEROGENEITY; COMPUTER MODEL; EPITHELIUM CELL; GENE EXPRESSION; HEMATOPOIETIC STEM CELL; HUMAN; IMMUNOCOMPETENT CELL; IMMUNOPHENOTYPING; MICROARRAY ANALYSIS; RNA SEQUENCE; SOLID MALIGNANT NEOPLASM; STROMA CELL; TRANSCRIPTOMICS; TUMOR GENE; TUMOR MICROENVIRONMENT; ANTIBODY SPECIFICITY; CELLS; COMPUTER SIMULATION; FLOW CYTOMETRY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NEOPLASM; PATHOLOGY; REPRODUCIBILITY; SOFTWARE;

EID: 85034614124     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1349-1     Document Type: Article
Times cited : (2788)

References (44)
  • 1
    • 33749319703 scopus 로고    scopus 로고
    • Type, density, and location of immune cells within human colorectal tumors predict clinical outcome
    • Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pagès C, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science. 2006;313:1960-4.
    • (2006) Science , vol.313 , pp. 1960-1964
    • Galon, J.1    Costes, A.2    Sanchez-Cabo, F.3    Kirilovsky, A.4    Mlecnik, B.5    Lagorce-Pagès, C.6
  • 2
    • 84858590826 scopus 로고    scopus 로고
    • Accessories to the crime: functions of cells recruited to the tumor microenvironment
    • Hanahan D, Coussens LM. Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell. 2012;21:309-22.
    • (2012) Cancer Cell , vol.21 , pp. 309-322
    • Hanahan, D.1    Coussens, L.M.2
  • 3
    • 84938984463 scopus 로고    scopus 로고
    • The prognostic landscape of genes and infiltrating immune cells across human cancers
    • Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, et al. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med. 2015;21:938-45.
    • (2015) Nat Med , vol.21 , pp. 938-945
    • Gentles, A.J.1    Newman, A.M.2    Liu, C.L.3    Bratman, S.V.4    Feng, W.5    Kim, D.6
  • 4
    • 67749112023 scopus 로고    scopus 로고
    • Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus
    • Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z, Clark HF. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One. 2009;4:e6098.
    • (2009) PLoS One , vol.4
    • Abbas, A.R.1    Wolslegel, K.2    Seshasayee, D.3    Modrusan, Z.4    Clark, H.F.5
  • 5
    • 84898018919 scopus 로고    scopus 로고
    • Computational deconvolution: extracting cell type-specific information from heterogeneous samples
    • Shen-Orr SS, Gaujoux R. Computational deconvolution: extracting cell type-specific information from heterogeneous samples. Curr Opin Immunol. 2013;25:571-8.
    • (2013) Curr Opin Immunol , vol.25 , pp. 571-578
    • Shen-Orr, S.S.1    Gaujoux, R.2
  • 6
    • 84920962202 scopus 로고    scopus 로고
    • Molecular and genetic properties of tumors associated with local immune cytolytic activity
    • Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48-61.
    • (2015) Cell , vol.160 , pp. 48-61
    • Rooney, M.S.1    Shukla, S.A.2    Wu, C.J.3    Getz, G.4    Hacohen, N.5
  • 8
    • 84976438403 scopus 로고    scopus 로고
    • High-throughput genomic profiling of tumor-infiltrating leukocytes
    • Newman AM, Alizadeh AA. High-throughput genomic profiling of tumor-infiltrating leukocytes. Curr Opin Immunol. 2016;41:77-84.
    • (2016) Curr Opin Immunol , vol.41 , pp. 77-84
    • Newman, A.M.1    Alizadeh, A.A.2
  • 9
    • 84931426001 scopus 로고    scopus 로고
    • Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy
    • Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, et al. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 2015;16:64.
    • (2015) Genome Biol , vol.16 , pp. 64
    • Angelova, M.1    Charoentong, P.2    Hackl, H.3    Fischer, M.L.4    Snajder, R.5    Krogsdam, A.M.6
  • 10
    • 84983347823 scopus 로고    scopus 로고
    • Comprehensive analyses of tumor immunity: implications for cancer immunotherapy
    • Li B, Severson E, Pignon J-C, Zhao H, Li T, Novak J, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016;17:14.
    • (2016) Genome Biol , vol.17 , pp. 14
    • Li, B.1    Severson, E.2    Pignon, J.-C.3    Zhao, H.4    Li, T.5    Novak, J.6
  • 12
    • 85009106590 scopus 로고    scopus 로고
    • Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade
    • Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18:248-62.
    • (2017) Cell Rep , vol.18 , pp. 248-262
    • Charoentong, P.1    Finotello, F.2    Angelova, M.3    Mayer, C.4    Efremova, M.5    Rieder, D.6
  • 13
    • 85002930854 scopus 로고    scopus 로고
    • Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
    • Şenbabaoğlu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, et al. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2016;17:231.
    • (2016) Genome Biol , vol.17 , pp. 231
    • Şenbabaoğlu, Y.1    Gejman, R.S.2    Winer, A.G.3    Liu, M.4    Allen, E.M.5    Velasco, G.6
  • 14
    • 84903768676 scopus 로고    scopus 로고
    • Tackling the cancer stem cells--what challenges do they pose?
    • Pattabiraman DR, Weinberg RA. Tackling the cancer stem cells--what challenges do they pose? Nat Rev Drug Discov. 2014;13:497-512.
    • (2014) Nat Rev Drug Discov , vol.13 , pp. 497-512
    • Pattabiraman, D.R.1    Weinberg, R.A.2
  • 15
    • 84945451852 scopus 로고    scopus 로고
    • Immunological hallmarks of stromal cells in the tumour microenvironment
    • Turley SJ, Cremasco V, Astarita JL. Immunological hallmarks of stromal cells in the tumour microenvironment. Nat Rev Immunol. 2015;15:669-82.
    • (2015) Nat Rev Immunol , vol.15 , pp. 669-682
    • Turley, S.J.1    Cremasco, V.2    Astarita, J.L.3
  • 19
    • 85034586437 scopus 로고    scopus 로고
    • Accessed 3 May 2016.
    • Blueprint Epigenome Project. 2015. http://www.blueprint-epigenome.eu/. Accessed 3 May 2016.
    • (2015)
  • 20
    • 21344446363 scopus 로고    scopus 로고
    • Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data
    • Abbas AR, Baldwin D, Ma Y, Ouyang W, Gurney A, Martin F, et al. Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immune. 2005;6:319-31.
    • (2005) Genes Immune , vol.6 , pp. 319-331
    • Abbas, A.R.1    Baldwin, D.2    Ma, Y.3    Ouyang, W.4    Gurney, A.5    Martin, F.6
  • 21
    • 78651486442 scopus 로고    scopus 로고
    • Densely interconnected transcriptional circuits control cell states in human hematopoiesis
    • Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell. 2011;144:296-309.
    • (2011) Cell , vol.144 , pp. 296-309
    • Novershtern, N.1    Subramanian, A.2    Lawton, L.N.3    Mak, R.H.4    Haining, W.N.5    McConkey, M.E.6
  • 22
    • 84884297351 scopus 로고    scopus 로고
    • An expression atlas of human primary cells: inference of gene function from coexpression networks
    • Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics. 2013;14:632.
    • (2013) BMC Genomics , vol.14 , pp. 632
    • Mabbott, N.A.1    Baillie, J.K.2    Brown, H.3    Freeman, T.C.4    Hume, D.A.5
  • 23
    • 84859169877 scopus 로고    scopus 로고
    • The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
    • Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483:603-7.
    • (2012) Nature , vol.483 , pp. 603-607
    • Barretina, J.1    Caponigro, G.2    Stransky, N.3    Venkatesan, K.4    Margolin, A.A.5    Kim, S.6
  • 24
    • 70449091786 scopus 로고    scopus 로고
    • Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
    • Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462:108-12.
    • (2009) Nature , vol.462 , pp. 108-112
    • Barbie, D.A.1    Tamayo, P.2    Boehm, J.S.3    Kim, S.Y.4    Moody, S.E.5    Dunn, I.F.6
  • 25
    • 0027160335 scopus 로고
    • Fluorescence spectral overlap compensation for any number of flow cytometry parameters
    • Bagwell CB, Adams EG. Fluorescence spectral overlap compensation for any number of flow cytometry parameters. Ann N Y Acad Sci. 1993;677:167-84.
    • (1993) Ann N Y Acad Sci , vol.677 , pp. 167-184
    • Bagwell, C.B.1    Adams, E.G.2
  • 26
    • 84907994039 scopus 로고    scopus 로고
    • Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis
    • Linsley PS, Speake C, Whalen E, Chaussabel D. Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. PLoS One. 2014;9:e109760.
    • (2014) PLoS One , vol.9
    • Linsley, P.S.1    Speake, C.2    Whalen, E.3    Chaussabel, D.4
  • 27
    • 84885724091 scopus 로고    scopus 로고
    • Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer
    • Bindea G, Mlecnik B, Tosolini M, Kirilovsky A, Waldner M, Obenauf AC, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39:782-95.
    • (2013) Immunity , vol.39 , pp. 782-795
    • Bindea, G.1    Mlecnik, B.2    Tosolini, M.3    Kirilovsky, A.4    Waldner, M.5    Obenauf, A.C.6
  • 28
    • 84963614956 scopus 로고    scopus 로고
    • Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
    • Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352:189-96.
    • (2016) Science , vol.352 , pp. 189-196
    • Tirosh, I.1    Izar, B.2    Prakadan, S.M.3    Wadsworth, M.H.4    Treacy, D.5    Trombetta, J.J.6
  • 31
    • 84949207578 scopus 로고    scopus 로고
    • Systematic pan-cancer analysis of tumour purity
    • Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015;6:8971.
    • (2015) Nat Commun , vol.6 , pp. 8971
    • Aran, D.1    Sirota, M.2    Butte, A.J.3
  • 32
    • 57249084011 scopus 로고    scopus 로고
    • Visualizing high-dimensional data using t-SNE
    • van der Maaten L, Hinton GE. Visualizing high-dimensional data using t-SNE. J Mach Learn Res. 2008;9:2579-605.
    • (2008) J Mach Learn Res , vol.9 , pp. 2579-2605
    • Maaten, L.1    Hinton, G.E.2
  • 33
    • 85034611364 scopus 로고    scopus 로고
    • Accessed 2 May
    • FANTOM5 project. http://fantom.gsc.riken.jp/5/. Accessed 2 May 2016.
    • (2016)
  • 34
    • 85034585282 scopus 로고    scopus 로고
    • Accessed 5 May
    • ENCODE: Encyclopedia of DNA Elements. https://www.encodeproject.org/. Accessed 5 May 2016.
    • (2016)
  • 35
    • 85034566649 scopus 로고    scopus 로고
    • Expression profiles from a variety of resting and activated human immune cells
    • Accessed 7 Nov 2014.
    • Abbas AR et al. Expression profiles from a variety of resting and activated human immune cells. 2010. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22886. Accessed 7 Nov 2014.
    • (2010)
    • Abbas, A.R.1
  • 36
    • 85034605408 scopus 로고    scopus 로고
    • Densely interconnected transcriptional circuits control cell states in human hematopoiesis
    • Accessed 11 Nov 2014.
    • Novershtern N et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. 2011. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24759. Accessed 11 Nov 2014.
    • (2011)
    • Novershtern, N.1
  • 37
    • 85034575478 scopus 로고    scopus 로고
    • An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks
    • Accessed 8 July 2016.
    • Mabbott NA et al. An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks. 2013. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49910. Accessed 8 July 2016.
    • (2013)
    • Mabbott, N.A.1
  • 38
    • 29144535372 scopus 로고    scopus 로고
    • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    • Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005;33:e175.
    • (2005) Nucleic Acids Res , vol.33
    • Dai, M.1    Wang, P.2    Boyd, A.D.3    Kostov, G.4    Athey, B.5    Jones, E.G.6
  • 39
    • 85034578304 scopus 로고    scopus 로고
    • Next generation sequencing of human immune cell subsets across diseases
    • Accessed 5 Jan 2017.
    • Speake C et al. Next generation sequencing of human immune cell subsets across diseases. 2015. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424. Accessed 5 Jan 2017.
    • (2015)
    • Speake, C.1
  • 40
    • 85034597453 scopus 로고    scopus 로고
    • Accessed 17 July 2016.
    • Immport. 2010. http://www.immport.org/immport-open/public/study/study/displayStudyDetail/SDY311. Accessed 17 July 2016.
    • (2010)
  • 41
    • 85034590293 scopus 로고    scopus 로고
    • Immport. 2010. http://www.immport.org/immport-open/public/study/study/displayStudyDetail/SDY420.
    • (2010)
  • 43
    • 84872202078 scopus 로고    scopus 로고
    • GSVA: gene set variation analysis for microarray and RNA-seq data
    • Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7.
    • (2013) BMC Bioinformatics , vol.14 , pp. 7
    • Hänzelmann, S.1    Castelo, R.2    Guinney, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.