SCPortalen: Human and mouse single-cell centric database

Nucleic Acids Research

Volumn 46, Issue D1, 2018, Pages D781-D787

  Abugessaisa, Imad ^a   Noguchi, Shuhei ^a   Böttcher, Michael ^a   Hasegawa, Akira ^a   Kouno, Tsukasa ^a   Kato, Sachi ^a   Tada, Yuhki ^a   Ura, Hiroki ^a   Abe, Kuniya ^a   Shin, Jay W ^a   Plessy, Charles ^a   Carninci, Piero ^a   Kasukawa, Takeya ^a  

^a RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS SOFTWARE; DATA BASE; GENE EXPRESSION; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; MOLECULAR GENETICS; MOLECULAR IMAGING; PRIORITY JOURNAL; SCPORTALEN DATABASE; SEQUENCE ANALYSIS; ANIMAL; COMPUTER INTERFACE; GENE ONTOLOGY; GENETIC DATABASE; GENETICS; HUMAN; MEASUREMENT ACCURACY; MOUSE; SINGLE CELL ANALYSIS; WORKFLOW;

TRANSCRIPTOME;

ANIMALS; DATA ACCURACY; DATA CURATION; DATABASES, GENETIC; DATASETS AS TOPIC; GENE EXPRESSION; GENE ONTOLOGY; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; SINGLE-CELL ANALYSIS; TRANSCRIPTOME; USER-COMPUTER INTERFACE; WORKFLOW;

EID: 85040953474     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx949     Document Type: Article

References (19)

1. Yuan, G.C., Cai, L., Elowitz, M., Enver, T., Fan, G., Guo, G., Irizarry, R., Kharchenko, P., Kim, J., Orkin, S., et al. (2017) Challengesand emerging directions in single-cell analysis. Genome Biol., 18, 84.
2. Cochrane, G., Karsch-Mizrachi, I., Nakamura, Y., InternationalNucleotide Sequence Database, C. (2011) The internationalnucleotide sequence database collaboration. Nucleic Acids Res., 39, D15-D18.
3. Jolliffe, I.T., Cadima, J. (2016) Principal component analysis: Areview and recent developments. Philos. Trans. A Math. Phys. Eng.Sci., 374, 20150202.
4. Van Der Maaten, L and Hinton, G. (2008) Visualizinghigh-dimensional data using t-sne. journal of machine learningresearch. J. Mach. Learn. Res., 9, 26.
5. Abugessaisa, I., Saevarsdottir, S., Tsipras, G., Lindblad, S., Sandin, C., Nikamo, P., Stahle, M., Malmstrom, V., Klareskog, L., Tegner, J.(2014) Accelerating translational research by clinically drivendevelopment of an informatics platform-a case study. PLoS One, 9, e104382.
6. Leinonen, R., Akhtar, R., Birney, E., Bonfield, J., Bower, L., Corbett, M., Cheng, Y., Demiralp, F., Faruque, N., Goodgame, N., et al.(2010) Improvements to services at the European Nucleotide Archive.Nucleic Acids Res., 38, D39-D45.
7. Coordinators, N.R. (2017) Database resources of the national centerfor biotechnology information. Nucleic Acids Res., 45, D12-D17.
8. Meehan, T.F., Masci, A.M., Abdulla, A., Cowell, L.G., Blake, J.A., Mungall, C.J., Diehl, A.D. (2011) Logical development of the cellontology. BMC Bioinformatics, 12, 6.
9. Sarntivijai, S., Lin, Y., Xiang, Z., Meehan, T.F., Diehl, A.D., Vempati, U.D., Schurer, S.C., Pang, C., Malone, J., Parkinson, H., et al.(2014) CLO: The cell line ontology. J. Biomed. Semantics, 5, 37.
10. Mungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E. andHaendel, M.A. (2012) Uberon, an integrative multi-species anatomyontology. Genome Biol., 13, R5.
11. Abugessaisa, I.E.A., Sivertun, A. (2004) Ontological approachtomodeling information systems The Fourth International Conferenceon Computer and Information Technology, CIT'04. IEEE, Wuhan, pp.1122-1127.
12. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R. (2013) STAR: Ultrafastuniversal RNA-seq aligner. Bioinformatics, 29, 15-21.
13. Liao, Y., Smyth, G.K., Shi, W. (2014) featureCounts: An efficientgeneral purpose program for assigning sequence reads to genomicfeatures. Bioinformatics, 30, 923-930.
14. Dennis, G. Jr, Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., Lempicki, R.A. (2003) DAVID: Database forannotation, visualization, and integrated discovery. Genome Biol., 4, P3.
15. Whitfield, M.L., Sherlock, G., Saldanha, A.J., Murray, J.I., Ball, C.A., Alexander, K.E., Matese, J.C., Perou, C.M., Hurt, M.M., Brown, P.O.et al. (2002) Identification of genes periodically expressed in thehuman cell cycle and their expression in tumors. Mol. Biol. Cell, 13, 1977-2000.
16. Tung, P.Y., Blischak, J.D., Hsiao, C.J., Knowles, D.A., Burnett, J.E., Pritchard, J.K., Gilad, Y. (2017) Batch effects and the effectivedesign of single-cell gene expression studies. Sci. Rep., 7, 39921.
17. Broman, K.W. (2015) R/qtlcharts: Interactive graphics forquantitative trait locus mapping. Genetics, 199, 359-361.
18. Gaublomme, J.T., Yosef, N., Lee, Y., Gertner, R.S., Yang, L.V., Wu, C., Pandolfi, P.P., Mak, T., Satija, R., Shalek, A.K., et al. (2015) Single-cellgenomics unveils critical regulators of Th17 cell pathogenicity. Cell, 163, 1400-1412.
19. Cote, R.G., Jones, P., Apweiler, R., Hermjakob, H. (2006) TheOntology Lookup Service, a lightweight cross-platform tool forcontrolled vocabulary queries. BMC Bioinformatics, 7, 97.