Anders, S., Pyl, P.T., and Huber, W. (2014). HTSeq—a Python framework to work with highthroughput sequencing data. Bioinformatics 31, 166-169.
Boeva, V., Louis-Brennetot, C., Peltier, A., Durand, S., Pierre-Eugene, C., Raynal, V.,
Etchevers, H.C., Thomas, S., Lermine, A., Daudigeos-Dubus, E., et al. (2017). Heterogeneity
of neuroblastoma cell identity defined by transcriptional circuitries. Nat Genet 49, 1408-
1413.
Consortium, E.P. (2012). An integrated encyclopedia of DNA elements in the human genome.
Nature 489, 57-74.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson,
M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics
29, 15-21.
Durbin, A.D., Zimmerman, M.W., Dharia, N.V., Abraham, B.J., Iniguez, A.B., WeichertLeahey, N., He, S., Krill-Burger, J.M., Root, D.E., Vazquez, F., et al. (2018). Selective gene
dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory
circuitry. Nat Genet 50, 1240-1246.
Frankish, A., Diekhans, M., Ferreira, A.M., Johnson, R., Jungreis, I., Loveland, J., Mudge,
J.M., Sisu, C., Wright, J., Armstrong, J., et al. (2019). GENCODE reference annotation for
the human and mouse genomes. Nucleic Acids Res 47, D766-D773.
Hemming, M.L., Lawlor, M.A., Zeid, R., Lesluyes, T., Fletcher, J.A., Raut, C.P., Sicinska,
E.T., Chibon, F., Armstrong, S.A., Demetri, G.D., et al. (2018). Gastrointestinal stromal
tumor enhancers support a transcription factor network predictive of clinical outcome. Proc
Natl Acad Sci U S A 115, E5746-E5755.
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat
Methods 9, 357-359.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G.,
Durbin, R., and Genome Project Data Processing, S. (2009). The Sequence Alignment/Map
format and SAMtools. Bioinformatics 25, 2078-2079.
Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and
dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing
reads. EMBnetjournal 17, 10.
Pantano, L. (2017). DEGreport: Report of DEG analysis.
Robinson, J.T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and
Mesirov, J.P. (2011). Integrative genomics viewer. Nat Biotechnol 29, 24-26.
Tsankov, A.M., Gu, H., Akopian, V., Ziller, M.J., Donaghey, J., Amit, I., Gnirke, A., and
Meissner, A. (2015). Transcription factor binding dynamics during human ES cell
differentiation. Nature 518, 344-349.
Wang, L., Wang, S., and Li, W. (2012). RSeQC: quality control of RNA-seq experiments.
Bioinformatics 28, 2184-2185.
Yu, G., and He, Q.Y. (2016). ReactomePA: an R/Bioconductor package for reactome pathway
analysis and visualization. Mol Biosyst 12, 477-479.
Yu, G., Wang, L.G., Han, Y., and He, Q.Y. (2012). clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284-287.
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