Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome
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) 1/ f(alpha) decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent alpha approximately 1 ext...
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| Veröffentlicht in: | Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2005-04, Vol.71 (4 Pt 1), p.041910-041910, Article 041910 |
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| container_end_page | 041910 |
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| container_issue | 4 Pt 1 |
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| container_title | Physical review. E, Statistical, nonlinear, and soft matter physics |
| container_volume | 71 |
| creator | Li, Wentian Holste, Dirk |
| description | 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) 1/ f(alpha) decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent alpha approximately 1 extends to about 10(7) bases, one order of magnitude longer than has previously been observed. We further find that (iii) almost all human chromosomes exhibit a crossover from alpha(1) approximately 1 (1/ f (alpha(1))) at lower frequency to alpha(2) |
| doi_str_mv | 10.1103/PhysRevE.71.041910 |
| format | Article |
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We find that (i) 1/ f(alpha) decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent alpha approximately 1 extends to about 10(7) bases, one order of magnitude longer than has previously been observed. We further find that (iii) almost all human chromosomes exhibit a crossover from alpha(1) approximately 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 crossover 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 base long oscillation in human chromosome 21. The universal 1/ f(alpha) spectrum in the human genome is further substantiated by a resistance to reduction in variance of guanine and cytosine content when the window size is increased.</description><identifier>ISSN: 1539-3755</identifier><identifier>EISSN: 1550-2376</identifier><identifier>DOI: 10.1103/PhysRevE.71.041910</identifier><identifier>PMID: 15903704</identifier><language>eng</language><publisher>United States</publisher><subject>Base Composition - genetics ; Chromosome Mapping - methods ; Chromosomes, Human - genetics ; Computer Simulation ; Crossing Over, Genetic - genetics ; DNA - genetics ; DNA Mutational Analysis - methods ; Humans ; Models, Chemical ; Models, Genetic ; Models, Statistical ; Pattern Recognition, Automated - methods ; Sequence Analysis, DNA - methods ; Stochastic Processes</subject><ispartof>Physical review. 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E, Statistical, nonlinear, and soft matter physics</title><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><description>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) 1/ f(alpha) decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent alpha approximately 1 extends to about 10(7) bases, one order of magnitude longer than has previously been observed. We further find that (iii) almost all human chromosomes exhibit a crossover from alpha(1) approximately 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 crossover 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 base long oscillation in human chromosome 21. The universal 1/ f(alpha) spectrum in the human genome is further substantiated by a resistance to reduction in variance of guanine and cytosine content when the window size is increased.</description><subject>Base Composition - genetics</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes, Human - genetics</subject><subject>Computer Simulation</subject><subject>Crossing Over, Genetic - genetics</subject><subject>DNA - genetics</subject><subject>DNA Mutational Analysis - methods</subject><subject>Humans</subject><subject>Models, Chemical</subject><subject>Models, Genetic</subject><subject>Models, Statistical</subject><subject>Pattern Recognition, Automated - methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Stochastic Processes</subject><issn>1539-3755</issn><issn>1550-2376</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpFkc1u2zAQhIkiReM4eYEeAp5yspwlKernGDhpUyBoi6I-CxS1sllIpKKVjPpJ8rqVf4qcdrGYb7CYYeyzgKUQoO5_bvf0C3dPy1QsIRa5gA9sJrSGSKo0uTjsKo9UqvUluyL6A6CkyuJP7FLoHFQK8Yy9rb3bYU-m4eK-5j44wgW3fSAKhzsPNSdrGuc3HP92waMfaMGNr7jd9qENFFqMqEPramd5Z4YBe3_ENqPxzmNk90OgaeE2-GHCufP88fsDJ3wd0Vs8ioct8u3YGs836CfLa_axNg3hzXnO2frL0-_Vc_Ty4-u31cNLZBWIIcq1qZSoyhK0rkHGVqoSUcbGZllc51gmVlVTDFrYJFaokhINgAZpMTcIqObs7uTb9WF6h4aidWSxaYzHMFKRpJmWIpOTUJ6Ex2x6rIuud63p94WA4lBH8b-OIhXFqY4Juj27j2WL1Ttyzl_9A3Vzizg</recordid><startdate>200504</startdate><enddate>200504</enddate><creator>Li, Wentian</creator><creator>Holste, Dirk</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>200504</creationdate><title>Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome</title><author>Li, Wentian ; Holste, Dirk</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c301t-95ad31dbb055f024c23bee24ac884f9eb6c3d15351c643e36bea00502ce9ae0e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Base Composition - genetics</topic><topic>Chromosome Mapping - methods</topic><topic>Chromosomes, Human - genetics</topic><topic>Computer Simulation</topic><topic>Crossing Over, Genetic - genetics</topic><topic>DNA - genetics</topic><topic>DNA Mutational Analysis - methods</topic><topic>Humans</topic><topic>Models, Chemical</topic><topic>Models, Genetic</topic><topic>Models, Statistical</topic><topic>Pattern Recognition, Automated - methods</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Stochastic Processes</topic><toplevel>online_resources</toplevel><creatorcontrib>Li, Wentian</creatorcontrib><creatorcontrib>Holste, Dirk</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Wentian</au><au>Holste, Dirk</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome</atitle><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><date>2005-04</date><risdate>2005</risdate><volume>71</volume><issue>4 Pt 1</issue><spage>041910</spage><epage>041910</epage><pages>041910-041910</pages><artnum>041910</artnum><issn>1539-3755</issn><eissn>1550-2376</eissn><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) 1/ f(alpha) decay is universally observed in the power spectra of all 24 chromosomes, and (ii) the exponent alpha approximately 1 extends to about 10(7) bases, one order of magnitude longer than has previously been observed. We further find that (iii) almost all human chromosomes exhibit a crossover from alpha(1) approximately 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 crossover 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 base long oscillation in human chromosome 21. The universal 1/ f(alpha) spectrum in the human genome is further substantiated by a resistance to reduction in variance of guanine and cytosine content when the window size is increased.</abstract><cop>United States</cop><pmid>15903704</pmid><doi>10.1103/PhysRevE.71.041910</doi><tpages>1</tpages></addata></record> |
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| ispartof | Physical review. E, Statistical, nonlinear, and soft matter physics, 2005-04, Vol.71 (4 Pt 1), p.041910-041910, Article 041910 |
| issn | 1539-3755 1550-2376 |
| language | eng |
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| source | MEDLINE; American Physical Society Journals |
| subjects | Base Composition - genetics Chromosome Mapping - methods Chromosomes, Human - genetics Computer Simulation Crossing Over, Genetic - genetics DNA - genetics DNA Mutational Analysis - methods Humans Models, Chemical Models, Genetic Models, Statistical Pattern Recognition, Automated - methods Sequence Analysis, DNA - methods Stochastic Processes |
| title | Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome |
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