Statistical Data Mining for Symbol Associations in Genomic Databases
Bernard Ycart,
Frederic Pont,
Jean-Jacques Fournie
Issue:
Volume 2, Issue 6, December 2014
Pages:
97-104
Received:
10 November 2014
Accepted:
28 November 2014
Published:
2 December 2014
Abstract: A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test assesses the significance of a group of symbols when found in several genesets of a given database. To each pair of symbols, a p-value depending on the frequency of the two symbols and on the number of joint occurrences, is associated. All pairs with p-values below a certain threshold define a graph structure on the set of symbols. The cliques of that graph are significant symbol associations, linked to a set of genesets where they can be found. The method can be applied to any database, and is illustrated on the MSigDB C2 database. Many of the symbol associations detected in C2 or in non-specific selections correspond to already known interactions. On more specific selections of C2, many previously unknown symbol associations have been detected. These associations unveal new candidates for gene or protein interactions, needing further investigation for biological evidence.
Abstract: A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test assesses the significance of a group of symbols when found in several genesets of a given database. To each pair of symbols, a p-value depending on the frequency of the two symbols and on the number of joint occurrences, is...
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The Processes of DNA Replication and the Shortening of the Telomere are Influenced by the Action of the Magnetic Field
Issue:
Volume 2, Issue 6, December 2014
Pages:
114-120
Received:
2 December 2014
Accepted:
11 December 2014
Published:
19 December 2014
Abstract: This hypothesis research work shows that the induction and the remanent phenomena of the magnetic properties govern the mechanism of the processes of DNA replication and the shortening of the telomere. The solenoid–like formation of each parental DNA strand, which exists at the initial stage of the replication process, enables an electric charge transformation through the strand to produce a magnetic field. The magnetic field, in turn, induces the surrounding medium to form a new (replicated) strand by a remanent magnetization. Through the remanent [residual] magnetization process, the replicated strand possesses a similar information pattern to that of the parental strand. In the same process, the remanent amount of magnetization forms the medium in which it has less of both repetitive and pattern magnetization than that of the parental strand, therefore the replicated strand shows a shortening in the length of its telomeres.
Abstract: This hypothesis research work shows that the induction and the remanent phenomena of the magnetic properties govern the mechanism of the processes of DNA replication and the shortening of the telomere. The solenoid–like formation of each parental DNA strand, which exists at the initial stage of the replication process, enables an electric charge tr...
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Ending the Karl Pearson Controversy (1904): Over the Incomplete Couplets Produced by Mendel’s Fraction-Addition Method
Issue:
Volume 2, Issue 6, December 2014
Pages:
121-125
Received:
28 November 2014
Accepted:
23 December 2014
Published:
6 January 2015
Abstract: Early in the 20th Century, leading mathematicians found a link between Mendel’s Laws and Newton’s Binomial. This enabled multigenerational studies of entire populations. In this regard, K. Pearson in 1904 raised objections to Mendel’s predictions that the ‘pure’ (dominant and recessive) descendants of hybrid ancestors turn out to be incomplete assemblies when using the sum of fractions used by Mendel in his 1866 article “Experiments in Plant Hybridization”. This algorithm is analyzed as a model for the case of just one hereditary characteristic, within an axiomatic framework that necessitates the formulation of a theorem in order to elucidate whether it was, on the one hand, a genuine mistake or, on the other, it is what Mendel, with all conviction and consideration, intended to say. We take into account the contemporary (1850-1870) knowledge of the cell and the structures involved in the transmission of inherited characteristics that this pioneer in the field of genetics would have had available for his deliberations at a time when this discipline was not yet a science. There follows the analysis of an unspecified intermediate member of the sum of fractions (not included in the Mendel’s original paper), which, from a mathematical standpoint, helps us resolve the incomplete assemblies (‘pure’ descendants) enigma.
Abstract: Early in the 20th Century, leading mathematicians found a link between Mendel’s Laws and Newton’s Binomial. This enabled multigenerational studies of entire populations. In this regard, K. Pearson in 1904 raised objections to Mendel’s predictions that the ‘pure’ (dominant and recessive) descendants of hybrid ancestors turn out to be incomplete asse...
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