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Gallagher, Richard J.; Lee, Eva K.; Patterson, David A.

doi:10.1023/a:1018943025993

Cited by 33 publications

(4 citation statements)

References 30 publications

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“…A numeric vector representing the frequency of occurrence of each of the seven DNA patterns was constructed for each sequence in the training set and used as input for discriminant analysis to develop a predictive rule. The training set consisted of the same 18 CpG islands (nine methylationprone, nine methylation-resistant) used for the pattern recognition module, and the classification algorithm was a linear program optimization-based discriminant analysis method (30,31). The accuracy of the resulting classifier was estimated by 10-fold cross-validation.…”

Section: Fig 2 Methylation Analysis Of Representative Rlgs Fragmentmentioning

confidence: 99%

Predicting aberrant CpG island methylation

Feltus

Lee

Costello

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

251

175

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Epigenetic silencing associated with aberrant methylation of promoter region CpG islands is one mechanism leading to loss of tumor suppressor function in human cancer. Profiling of CpG island methylation indicates that some genes are more frequently methylated than others, and that each tumor type is associated with a unique set of methylated genes. However, little is known about why certain genes succumb to this aberrant event. To address this question, we used Restriction Landmark Genome Scanning to analyze the susceptibility of 1,749 unselected CpG islands to de novo methylation driven by overexpression of DNA cytosine-5-methyltransferase 1 (DNMT1). We found that although the overall incidence of CpG island methylation was increased in cells overexpressing DNMT1, not all loci were equally affected. The majority of CpG islands (69.9%) were resistant to de novo methylation, regardless of DNMT1 overexpression. In contrast, we identified a subset of methylation-prone CpG islands (3.8%) that were consistently hypermethylated in multiple DNMT1 overexpressing clones. Methylation-prone and methylation-resistant CpG islands were not significantly different with respect to size, C؉G content, CpG frequency, chromosomal location, or promoter association. We used DNA pattern recognition and supervised learning techniques to derive a classification function based on the frequency of seven novel sequence patterns that was capable of discriminating methylation-prone from methylation-resistant CpG islands with 82% accuracy. The data indicate that CpG islands differ in their intrinsic susceptibility to de novo methylation, and suggest that the propensity for a CpG island to become aberrantly methylated can be predicted based on its sequence context.

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Section: Fig 2 Methylation Analysis Of Representative Rlgs Fragmentmentioning

confidence: 99%

Predicting aberrant CpG island methylation

Feltus

Lee

Costello

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

251

175

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“…Now I wandered in fairy caverns among the bones of primaeval monsters." 47 Bored and stifled on the workroom floor, he allows his mind to be peopled with "a rabble of phantasms" rising from things he has read.…”

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confidence: 99%

“…And as the self-indulgent habit grew on me, I began to live two lives-one mechanical and outward, one inward and imaginative. 48 Alton's brutish life in the rag trade is transformed by these protean dream analogues. The thread going through the needle becomes illusory as the Tropics, Greece, imaginary events, and phantoms become increasingly real.…”

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confidence: 99%

“…Dissatisfied with the unrecorded nature of his speculations, he gravitates to art first, then poetry, to transform them into "permanent independent things." 49 The "grace of rhythm and rhyme" 50 is a corollary to his ability to conjure up dreams. Locked out from the University of Cambridge due to class injustice as Alton Locke may have been, the sickness and suffering of his work, he claims, is the classroom and crucible where the onrush of novel or recombinant images can finally be artfully composed.…”

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To Write Like a Dream: Nineteenth-Century Legacies

Mukherjee¹

2019

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The gorgeous and wonderful reality of Venice is beyond the fancy of the wildest dreamer. Opium couldn't build such a place, and enchantment couldn't shadow it forth in a vision." 1 This is Charles Dickens in a letter to his friend John Forster, dated November 12, 1844, and dispatched from Venice. The author had come to Venice in a state of eager anticipation, his curiosity whetted by historical as well as fictional accounts. He reminds his old friend of his own tendency to have his "over-expectation" get the better of him, but this, he says, can never be the case with Venice, "a thing you would shed tears to see." 2 But what is it that makes Venice so phantasmagoric, always exceeding its representation in words and pictures? Dickens lists the reasons as if in a trance: the contrast between the solid reality of the houses and the "fever-madness" of the water; the "insupportable" glory of the floating city; Venice's radiant daytime magic as well as its sprawling mental underground, livid with "judgement chambers, secret doors, deadly nooks . . . vast churches, and old tombs." "[A] new sensation, a new memory, a new mind came upon me. Venice is a bit of my brain from this time," Dickens speculates. 3 In Dickens's "An Italian Dream," the restive traveller (sleeping very little at night, by his own confession, and never during the day) uses the noun and verb forms of "dream" in a variety of ways, some of which contradict each other. The intrepid traveller's sensory overload of an "unbroken succession of novelties" is comparable, he says, to the recall of "half-formed dreams." 4 In a pattern we see repeated in several works of nineteenth-century fiction and poetry, dreaming is not only related to movement and travel but depicted as dynamic itself: the shudders of the coach make some recollections disappear from the mind of the half-asleep author, while others come rushing in. The black boat, which he boards after the coach ride, marks a "dreamy kind of track" 5 towards the mysterious lights shining like tapers on the dark waves.The Italian dream, referred to simply as "the Dream" is a fugue 6 state between sleep and wakefulness, activity and passivity, aesthetic reception

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Predictive Analytics: Classification in Medicine and Biology

Lee

2016

Healthcare Analytics: From Data to Knowledge to Healthcare Improvement

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Cited by 33 publications

References 30 publications

Predicting aberrant CpG island methylation

Predicting aberrant CpG island methylation

To Write Like a Dream: Nineteenth-Century Legacies

Predictive Analytics: Classification in Medicine and Biology

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