Ashburner, M, Ball, CA, Blake, JA, Botstein, D, Butler, H, Cherry, JM, Davis, AP, Dolinski, K, Dwight, SS, Eppig, JT, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
Google Scholar |
Crossref |
Medline |
ISI
Bingham, C, Arbogast, B, Guillaume, GC, Lee, JK, Halberg, F (1982) Inferential statistical methods for estimating and comparing cosinor parameters. Chronobiologia 9:397-439.
Google Scholar |
Medline
Ceglia, N, Liu, Y, Chen, S, Agostinelli, F, Eckel-Mahan, K, Sassone-Corsi, P, Baldi, P (2018) CircadiOmics: circadian omic web portal. Nucleic Acids Res 46:W157-W162.
Google Scholar |
Crossref |
Medline
Cenek, L, Klindziuk, L, Lopez, C, McCartney, E, Martin Burgos, B, Tir, S, Harrington, ME, Leise, TL (2020) CIRCADA: shiny apps for exploration of experimental and synthetic circadian time series with an educational emphasis. J Biol Rhythms 35:214-222.
Google Scholar |
SAGE Journals |
ISI
Cornelissen, G (2014) Cosinor-based rhythmometry. Theor Biol Med Model 11:16.
Google Scholar |
Crossref |
Medline |
ISI
de Leeuw, CA, Neale, BM, Heskes, T, Posthuma, D (2016) The statistical properties of gene-set analysis. Nat Rev Genet 17:353-364.
Google Scholar |
Crossref |
Medline
Ding, H, Meng, L, Liu, AC, Gumz, ML, Bryant, AJ, McClung, CA, Tseng, GC, Esser, KA, Huo, Z (2021) Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications. Brief Bioinform. doi:10.1093/bib/bbab224.
Google Scholar |
Crossref
Durinck, S, Moreau, Y, Kasprzyk, A, Davis, S, De Moor, B, Brazma, A, Huber, W (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21:3439-3440.
Google Scholar |
Crossref |
Medline |
ISI
Durinck, S, Spellman, PT, Birney, E, Huber, W (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc 4:1184-1191.
Google Scholar |
Crossref |
Medline |
ISI
Gene Ontology Consortium (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res 49:D325-D334.
Google Scholar |
Crossref |
Medline
Hughes, ME, Hogenesch, JB, Kornacker, K (2010) JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms 25:372-380.
Google Scholar |
SAGE Journals |
ISI
Kanehisa, M (2019) Toward understanding the origin and evolution of cellular organisms. Protein Sci 28:1947-1951.
Google Scholar |
Crossref |
Medline
Kanehisa, M, Goto, S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30.
Google Scholar |
Crossref |
Medline |
ISI
Kanehisa, M, Furumichi, M, Sato, Y, Ishiguro-Watanabe, M, Tanabe, M (2021) KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 49:D545-D551.
Google Scholar |
Crossref |
Medline
Kramer, A, Green, J, Pollard, J, Tugendreich, S (2014) Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 30:523-530.
Google Scholar |
Crossref |
Medline |
ISI
Li, S, Shui, K, Zhang, Y, Lv, Y, Deng, W, Ullah, S, Zhang, L, Xue, Y (2017) CGDB: a database of circadian genes in eukaryotes. Nucleic Acids Res 45:D397-D403.
Google Scholar |
Medline
Manella, G, Sabath, E, Aviram, R, Dandavate, V, Ezagouri, S, Golik, M, Adamovich, Y, Asher, G (2021) The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. Nat Metab 3:829-842.
Google Scholar |
Crossref |
Medline
Moskon, M (2020) CosinorPy: a python package for cosinor-based rhythmometry. BMC Bioinformatics 21:485.
Google Scholar |
Crossref |
Medline
Parsons, R, Parsons, R, Garner, N, Oster, H, Rawashdeh, O (2020) CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms. Bioinformatics 36:1208-1212.
Google Scholar |
Medline
Paschos, GK, Ibrahim, S, Song, WL, Kunieda, T, Grant, G, Reyes, TM, Bradfield, CA, Vaughan, CH, Eiden, M, Masoodi, M, et al. (2012) Obesity in mice with adipocyte-specific deletion of clock component Arntl. Nat Med 18:1768-1777.
Google Scholar |
Crossref |
Medline |
ISI
Patke, A, Young, MW, Axelrod, S (2020) Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 21:67-84.
Google Scholar |
Crossref |
Medline
Pelikan, A, Herzel, H, Kramer, A, Ananthasubramaniam, B (2021) Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS J. doi:10.1111/febs.16095.
Google Scholar
Pizarro, A, Hayer, K, Lahens, NF, Hogenesch, JB (2013) CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res 41:D1009-D1013.
Google Scholar |
Crossref |
Medline |
ISI
Sehgal, A (2017) Physiology flies with time. Cell 171:1232-1235.
Google Scholar |
Crossref |
Medline
Simillion, C, Liechti, R, Lischer, HE, Ioannidis, V, Bruggmann, R (2017) Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC Bioinformatics 18:151.
Google Scholar |
Crossref |
Medline
Singer, JM, Hughey, JJ (2019) LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data. J Biol Rhythms 34:5-18.
Google Scholar |
SAGE Journals |
ISI
Takahashi, JS (2017) Transcriptional architecture of the mammalian circadian clock. Nat Rev Genet 18:164-179.
Google Scholar |
Crossref |
Medline
Tenenbaum, D, Maintainer, B (2021) KEGGREST: client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) (R package version 1.32.0). doi:
10.18129/B9.bioc.KEGGREST.
Google Scholar |
Crossref
Thaben, PF, Westermark, PO (2014) Detecting rhythms in time series with RAIN. J Biol Rhythms 29:391-400.
Google Scholar |
SAGE Journals |
ISI
Thaben, PF, Westermark, PO (2016) Differential rhythmicity: detecting altered rhythmicity in biological data. Bioinformatics 32:2800-2808.
Google Scholar |
Crossref |
Medline |
ISI
Weger, BD, Gobet, C, David, FPA, Atger, F, Martin, E, Phillips, NE, Charpagne, A, Weger, M, Naef, F, Gachon, F (2021) Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proc Natl Acad Sci U S A 118:e2015803118.
Google Scholar |
Crossref |
Medline
Wu, G, Anafi, RC, Hughes, ME, Kornacker, K, Hogenesch, JB (2016) MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics 32:3351-3353.
Google Scholar |
Crossref |
Medline |
ISI
Xin, H, Deng, F, Zhou, M, Huang, R, Ma, X, Tian, H, Tan, Y, Chen, X, Deng, D, Shui, G, et al. (2021) A multi-tissue multi-omics analysis reveals distinct kineztics in entrainment of diurnal transcriptomes by inverted feeding. iScience 24:102335.
Google Scholar |
Crossref |
Medline
Yang, G, Chen, L, Grant, GR, Paschos, G, Song, WL, Musiek, ES, Lee, V, McLoughlin, SC, Grosser, T, Cotsarelis, G, et al. (2016) Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Sci Transl Med 8:324ra16.
Google Scholar |
Crossref |
Medline |
ISI
Zhang, R, Lahens, NF, Ballance, HI, Hughes, ME, Hogenesch, JB (2014) A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A 111:16219-16224.
Google Scholar |
Crossref |
Medline |
ISI
Zielinski, T, Moore, AM, Troup, E, Halliday, KJ, Millar, AJ (2014) Strengths and limitations of period estimation methods for circadian data. PLoS ONE 9:e96462.
Google Scholar |
Crossref |
Medline |
ISI
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