dorsal/arxiv
View SchemaUniversal 1/f noise, cross-overs of scaling exponents, and chromosome specific patterns of GC content in DNA sequences of the human genome
| Authors | Wentian Li, Dirk Holste |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0411016 |
| URL | https://arxiv.org/abs/q-bio/0411016 |
| DOI | 10.1103/PhysRevE.71.041910 |
| Journal | Physical Review E, 71, 041910 (2005) |
Abstract
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all twenty-four chromosomes, and that (ii) the exponent alpha \approx 1 extends to about 10^7 bases, one order of magnitude longer than what has previously been observed. We further find that (iii) almost all human chromosomes exhibit a cross-over from alpha_1 \approx 1 (1/f^alpha_1) at lower frequency to alpha_2 < 1 (1/f^alpha_2) at higher frequency, typically occurring at around 30,000--100,000 bases, while (iv) the cross-over in this frequency range is virtually absent in human chromosome 22. In addition to the universal 1/f^alpha noise in power spectra, we find (v) several lines of evidence for chromosome-specific correlation structures, including a 500,000 bases long oscillation in human chromosome 21. The universal 1/f^alpha spectrum in human genome is further substantiated by a resistance to variance reduction in guanine and cytosine content when the window size is increased.
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"abstract": "Spatial fluctuations of guanine and cytosine base content (GC%) are studied\nby spectral analysis for the complete set of human genomic DNA sequences. We\nfind that (i) the 1/f^alpha decay is universally observed in the power spectra\nof all twenty-four chromosomes, and that (ii) the exponent alpha \\approx 1\nextends to about 10^7 bases, one order of magnitude longer than what has\npreviously been observed. We further find that (iii) almost all human\nchromosomes exhibit a cross-over from alpha_1 \\approx 1 (1/f^alpha_1) at lower\nfrequency to alpha_2 \u003c 1 (1/f^alpha_2) at higher frequency, typically occurring\nat around 30,000--100,000 bases, while (iv) the cross-over in this frequency\nrange is virtually absent in human chromosome 22. In addition to the universal\n1/f^alpha noise in power spectra, we find (v) several lines of evidence for\nchromosome-specific correlation structures, including a 500,000 bases long\noscillation in human chromosome 21. The universal 1/f^alpha spectrum in human\ngenome is further substantiated by a resistance to variance reduction in\nguanine and cytosine content when the window size is increased.",
"arxiv_id": "q-bio/0411016",
"authors": [
"Wentian Li",
"Dirk Holste"
],
"categories": [
"q-bio.GN",
"q-bio.BM"
],
"doi": "10.1103/PhysRevE.71.041910",
"journal_ref": "Physical Review E, 71, 041910 (2005)",
"title": "Universal 1/f noise, cross-overs of scaling exponents, and chromosome specific patterns of GC content in DNA sequences of the human genome",
"url": "https://arxiv.org/abs/q-bio/0411016"
},
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