The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Cistrome: an integrative platform for transcriptional regulation studies
Open accessAbstract
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“In Cistrome, the ‘ Conservation Plot ’ tool can take one or more cistromes in BED files as input, and use UCSC PhastCons conservation scores [20] to produce a figure showing the average conservation score profiles around the peak centers (Figure 2d).”
MethodThe European nucleotide archive
Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq967 · Cited by 690 · cited 1×
“Currently, databases such as the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [33] and the European Bioinformatics Institute (EBI) ArrayExpress [34] host array data, and databases such as the NCBI Sequence Reads Archive (SRA) [35] and the EBI SRA host sequencing data [36].”
Cited by
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Chuong, E. B., Elde, N. C., & Feschotte, C. (2016) · Science · doi:10.1126/science.aad5497 · Cited by 1,008
Target analysis by integration of transcriptome and ChIP-seq data with BETA
Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang, Q., Meyer, C. A., Zhang, Y., & Liu, X. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.150 · Cited by 544
Self-citationThe androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis
Pomerantz, M. M., Li, F., Takeda, D. Y., Lenci, R., Chonkar, A., Chabot, M., Cejas, P., Vazquez, F., Cook, J., Shivdasani, R. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3419 · Cited by 470
Self-citationEndogenous retroviruses function as species-specific enhancer elements in the placenta
Chuong, E. B., Rumi, M. A. K., Soares, M. J., & Baker, J. C. (2013) · Nature Genetics · doi:10.1038/ng.2553 · Cited by 429
Metadata
- Authors
- Liu, T., Ortiz, J. A., Taing, L., Meyer, C. A., Lee, B., Zhang, Y., Shin, H., Wong, S. S., Ma, J., Lei, Y., Pape, U. J., Poidinger, M., Chen, Y., Yeung, K., Brown, M., Turpaz, Y., & Liu, X. S.
- Venue
- Genome Biology
- Published
- 2011-08-22
- Volume
- 12
- Issue
- 8
- Pages
- R83-R83
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2125362831
- Cited by
- 716
- References
- 5
- FWCI
- 16.46
- Type
- journal article
- Language
- en
- Open access
- gold
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- Liu, T., Ortiz, J. A., Taing, L., Meyer, C. A., Lee, B., Zhang, Y., Shin, H., Wong, S. S., Ma, J., Lei, Y., Pape, U. J., Poidinger, M., Chen, Y., Yeung, K., Brown, M., Turpaz, Y., & Liu, X. S. (2011). Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology. https://doi.org/10.1186/gb-2011-12-8-r83
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