CellAtlasSearch: A scalable search engine for single cells

Nucleic Acids Research

Volumn 46, Issue W1, 2018, Pages W141-W147

  Srivastava, Divyanshu ^a   Iyer, Arvind ^a   Kumar, Vibhor ^a   Sengupta, Debarka ^a  

^a INDRAPRASTHA INSTITUTE OF INFORMATION TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL DENSITY; CIRCULATING TUMOR CELL; GENERAL PRACTITIONER; HUMAN; INFORMATION PROCESSING; ONLINE SYSTEM; PRIORITY JOURNAL; REFERENCE DATABASE; SCIENTIST; SEARCH ENGINE; SINGLE CELL ANALYSIS; TRANSCRIPTOMICS; WEB BROWSER; ANIMAL; CELL LINE; COMPUTER INTERFACE; GENE EXPRESSION PROFILING; INTERNET; METABOLISM; MOUSE; PROCEDURES; TUMOR EMBOLISM;

ANIMALS; CELL LINE; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MICE; NEOPLASTIC CELLS, CIRCULATING; SEARCH ENGINE; SINGLE-CELL ANALYSIS; USER-COMPUTER INTERFACE;

EID: 85050864655     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky421     Document Type: Article

References (26)

1. Wagner, A., Regev, A. and Yosef, N. (2016) Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol., 34, 1145.
2. Grün, D., Lyubimova, A., Kester, L., Wiebrands, K., Basak, O., Sasaki, N., Clevers, H. and van Oudenaarden, A. (2015) Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature, 525, 251.
3. Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N. and Martersteck, E. M. (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 161, 1202-1214.
4. Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M. et al. (2017) The human cell atlas. Elife, 6, e27041.
5. Verhaak, R. G., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P. et al. (2010) Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell, 17, 98-110.
6. Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L. et al. (2014) Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science, 6, 1254257.
7. Collado-Torres, L., Nellore, A., Kammers, K., Ellis, S. E., Taub, M. A., Hansen, K. D., Jaffe, A. E., Langmead, B. and Leek, J. T. (2017) Reproducible RNA-seq analysis using recount2. Nat. Biotechnol., 35, 319.
8. Ner-Gaon, H., Melchior, A., Golan, N., Ben-Haim, Y. and Shay, T. (2017) JingleBells: a repository of immune-related single-cell RNA-sequencing datasets. J. Immunol., 198, 3375-3379.
9. Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H. and Horton, P. (2007) CellMontage: similar expression profile search server. Bioinformatics, 23, 3103-3104.
10. Zinman, G. E., Naiman, S., Kanfi, Y., Cohen, H. and Bar-Joseph, Z. (2013) ExpressionBlast: mining large, unstructured expression databases. Nat. Methods, 10, 925.
11. DeFreitas, T., Saddiki, H. and Flaherty, P. (2016) GEMINI: a computationally-efficient search engine for large gene expression datasets. BMC Bioinformatics, 17, 102.
12. Duan, Q., Reid, S. P., Clark, N. R., Wang, Z., Fernandez, N. F., Rouillard, A. D., Readhead, B., Tritsch, S. R., Hodos, R., Hafner, M. et al. (2016) L1000CDS 2: LINCS L1000 characteristic direction signatures search engine. NPJ Syst. Biol. Applic., 2, 16015.
13. Li, H., Courtois, E. T., Sengupta, D., Tan, Y., Chen, K. H., Goh, J. J. L., Kong, S. L., Chua, C., Hon, L. K., Tan, W. S. et al. (2017) Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat. Genet., 49, 708.
14. Sinha, D., Kumar, A., Kumar, H., Bandyopadhyay, S. and Sengupta, D. (2018) dropClust: efficient clustering of ultra-large scRNA-seq data. Nucleic Acids Res., 46, e36.
15. Edgar, R., Domrachev, M. and Lash, A. E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic acids research, 30, 207-210.
16. Indyk, P. and Motwani, R. (1998) Approximate nearest neighbors: towards removing the curse of dimensionality. In Proceedings of the thirtieth annual ACM Symposium on Theory of computing, ACMpp. 604-613.
17. Gionis, A., Indyk, P., Motwani, R. et al. (1999) Similarity search in high dimensions via hashing. VLDB, 99, 518-529.
18. Lee, H., Ng, R. T. and Shim, K. (2011) Similarity join size estimation using locality sensitive hashing. Proc. VLDB Endowment, 4, 338-349.
19. Jaskowiak, P. A., Campello, R. J. and Costa, I. G. (2014) On the selection of appropriate distances for gene expression data clustering. In BMC Bioinformatics, BioMed Central, Vol. 15, p. S2.
20. Zheng, G. X., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J. et al. (2017) Massively parallel digital transcriptional profiling of single cells. Nat. Commun., 8, 14049.
21. North, B. V., Curtis, D. and Sham, P. C. (2002) A note on the calculation of empirical P values from Monte Carlo procedures. Am. J. Hum. Genet., 71, 439.
22. Benjamin, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
23. Consortium, G. et al. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648-660.
24. Alix-Panabières, C. and Pantel, K. (2014) Challenges in circulating tumour cell research. Nat. Rev. Cancer, 14, 623.
25. Song, Y., Tian, T., Shi, Y., Liu, W., Zou, Y., Khajvand, T., Wang, S., Zhu, Z. and Yang, C. (2017) Enrichment and single-cell analysis of circulating tumor cells. Chem. Sci., 8, 1736-1751.
26. Zheng, Y., Miyamoto, D. T., Wittner, B. S., Sullivan, J. P., Aceto, N., Jordan, N. V., Yu, M., Karabacak, N. M., Comaills, V., Morris, R. et al. (2017) Expression of-globin by cancer cells promotes cell survival during blood-borne dissemination. Nat. Commun., 8, 14344.