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Topic: Gene selection

Related Topics

Group selection

Adaptationism

Stephen Jay Gould

Reductionist

	The Selfish Gene - Wikipedia, the free encyclopedia
		The phrase "selfish gene" in the title of the book was coined by Dawkins as a provocative way of expressing the gene-centered view of evolution, which holds that evolution can be viewed as acting on genes, and that selection on organisms or populations almost never overrides selection on genes.
		Genes that help the organism they are in to survive and reproduce also improve their own chances of being passed on; so most of the time "successful" genes will also be beneficial to the organism.
		In particular, phenomena such as kin selection and eusociality, where organisms act against their individual interests (in the sense of health, safety or personal reproduction) to help related organisms reproduce, can be explained as genes helping copies of themselves in other bodies to replicate.
	en.wikipedia.org /wiki/The_Selfish_Gene (923 words)

	Kin selection - Wikipedia, the free encyclopedia
		Kin selection was first suggested by Darwin as an explanation of the sterile castes of social insects and has later been mathematically defined by W.
		Under natural selection, a gene that causes itself to increase in frequency should become more common in the population.
		Kin selection has been used to explain the evolution of humanity's social structure, social insects such as ants and termites, and even the evolution of multicellular animals.
	en.wikipedia.org /wiki/Kin_selection (429 words)

	Gene selection - EvoWiki
		Gene selection or "selfish gene" theory is the theory that genes are the unit of selection.
		Gene selection theory is central to the understanding of contemporary evolutionary theory, and has developed from population genetics and the modern synthesis, and was established as the leading theory of natural selection during the Williams revolution.
		There is still some scientific debate about gene selection, which leading biologists such as Ernst Mayr rejecting the theory, though this is largely based on a misunderstanding of gene selection.
	wiki.cotch.net /index.php/Gene_selection (219 words)

	Regression analysis in optimal gene selection for DNA microarray analysis (Site not responding. Last check: 2007-10-20)
		It is important to select informative genes, which are related to cancer because not all genes are needed for classifying the cancer.
		The proposed method selects gene which is good at explaining the part that are not explainable by the former selected genes.
		Selecting genes with forward selection method is more powerful than the other gene selection methods in cancer prediction.
	www.iscb.org /ismb2003/posters/bonanzaATcandy.yonsei.ac.kr_285.html (328 words)

	Group selection - EvoWiki
		Group selection refers to the idea that alleles can become fixed or spread because of the benefits they bestow on groups, regardless of the fitness of individuals within that group.
		These responses were part of the lead up to the Williams Revolution in which gene selection theory became the prominent paradigm.
		Genetic variation, the raw material of selection, is much higher between individuals than it is between groups, particularly as groups grow larger.
	wiki.cotch.net /index.php/Group_selection (334 words)

	TRANSGENIC ART by Eduardo Kac
		Selective breeding is a long-term technique based on the indirect manipulation of the genetic material of two or more organisms and is responsible for many of the crops we eat and the livestock we raise.
		This means that artists now can not only combine genes from different species but easily write a DNA sequence on their word processors, email it to a commercial synthesis facility, and in less than a week receive a test tube with millions of molecules of DNA with the expected sequence.
		Genes have two important components: the structural element (which codes for a particular protein) and the regulatory element ("switches" that tell genes when and how to perform).
	www.ekac.org /transgenic.html (4406 words)

	BioMed Central \| Full text \| Entropy-based gene ranking without selection bias for the predictive classification of ...
		We have thus used a strategy for gene selection that is based on a saturation profile derived from an exponential approximation of the classification error, as estimated by the two-strata modeling scheme.
		The exponentially decreasing behavior we observed after correcting for selection bias is consistent with recent literature proposing that the relationship between cancer classification accuracy and gene ranking from microarray data may be modeled by a power-law function, also called a Zipf's law [22,25].
		Moreover, twelve genes (5, 9, 10, 21, 25, 34, 37, 44, 46, 56, 71, 73) are also listed as important in [21], four genes (9, 10, 22, 26) in [6], three genes (5, 9, 44) in [2], and 9 genes (5, 9, 21, 22, 28, 34, 44, 57, 71) in [4].
	www.biomedcentral.com /1471-2105/4/54 (7555 words)

	R-SVM : SVM Recursive Gene Selection and Classification (Site not responding. Last check: 2007-10-20)
		R-SVM : SVM Recursive Gene Selection and Classification
		The method uses SVM for both classification and for selecting a subset of relevant genes according to their relative contribution in the classification.
		This process is done recursively so that a series of gene subsets and classification models can be obtained in a recursive manner, at different levels of gene selection.
	www.biostat.harvard.edu /~xzhang/R-SVM/R-SVM.html (663 words)

	Virology Journal \| Full text \| Reference gene selection for quantitative real-time PCR analysis in virus infected ...
		To date, it is generally accepted, that the selection of the ideal reference gene in gene expression analysis has to be done for each individual experimental setting by evaluating several genes and using the best two or three of these genes as reference.
		TBP seems to be a relative stable expressed gene during the course of virus replication of different viruses in different cells.
		These genes are a good point to start reference gene selection in gene expression studies in virus infection experiments.
	www.virologyj.com /content/2/1/7 (1937 words)

	The Korea Times : Koreans Develop Software for Gene Screening (Site not responding. Last check: 2007-10-20)
		Genetic therapy is an emerging technique for correcting genes responsible for disease by replacing, augmenting or eliminating the missing or defective genes.
		Genes, the basic physical and functional units of heredity, are the sequences of bases that encode instructions on how to produce proteins.
		Although genes receive the most attention, proteins perform most of life's functions and many genetic disorders occur when the gene-encoded proteins fail to function normally.
	times.hankooki.com /lpage/200501/kt2005011716400853460.htm (346 words)

	Hygromycin.com, Antibiotics for Gene Selection and Cell Culture
		It is used for the selection and maintenance of prokaryotic and eukaryotic cells transfected with the hygromycin resistance gene, hph.
		Cloning of the resistance gene and fusion with eukaryotic promoters has resulted in the development of vectors that permit selection for resistance to Hygromycin B in both prokaryotic and eukaryotic cells.
		Commonly used concentrations for selection are 200 mg/ml for mammalian cells, 20-200 mg/ml for plant cells and bacteria cells and 200-1000 mg/ml for fungi.
	www.hygromycin.com (221 words)

	AG 2-2 Xu (Site not responding. Last check: 2007-10-20)
		Various approaches to gene selection for cancer classification based on microarray data can be found in the literature and they may be grouped into two categories: univariate methods and multivariate methods.
		However, the selection process of multivariate methods may be sensitive to the presence of irrelevant genes, random variations in the gene expression level and outliers in the training data.
		It is able to discover sets consisting of fewer genes than those reported in the literature and at the same time achieve the same or better prediction accuracy.
	www.openmindjournals.com /AG-2-2-Xu.htm (295 words)

	Database Development in Toxicogenomics: Issues and Efforts
		However, because of the relatively poor annotation of expressed genes and sequence tags, particularly in the dog and rat, the interpretation of transcript profiling experiments is challenging.
		The gene index will be developed in collaboration with other groups at the EBI and the established model organism databases, forming the basis of database integration.
		Such information will include all the synonyms by which a gene is known in different organisms, the toxicant responses identified for specific genes in different species, and a platform that promotes comparisons of gene sequences and toxicant activity among diverse organisms.
	ehp.niehs.nih.gov /txg/members/2004/6697/6697.html (9292 words)

	CHAPTER 13 NATURAL SELECTION
		Selecting which trait will be used (which is natural selection) is not evolution, for the trait was already at hand.
		The genes of the corn continue on from generation to generation, and only those ears in any given generation that are exposed to sunlight will have red kernels.
		In fact, natural selection is obviously misnamed: it is "natural variation," not "natural selection"—for it is only composed of simple variations, or gene reshuffling, within an existing species.
	www.evolution-facts.org /Ev-V2/2evlch13.htm (11425 words)

	The Selfish Gene - EvoWiki (Site not responding. Last check: 2007-10-20)
		The book argues that selection must be seen as acting on genes (gene selection) rather than individuals or groups, and debunks the idea that individuals act "for the good of the species".
		Dawkins collects all these techniques together to argue that all biologists should understand natural selection as actually operating on genes rather than as, traditionally thought, individual organisms, which Dawkins calls vehicles.
		The inference is that group selection is an invalid tool and all cases of biological altruism could be explained instead by gene selection, that is vehicles' altruism benefits selfish genes and so is not evolutionarily problematic, or indeed altruism, after all.
	www.evowiki.org /index.php/The_Selfish_Gene (216 words)

	BBC NEWS \| Health \| Concern over baby gene selection
		Parents might be able to choose their baby's IQ Parents should not be allowed to select embryos for IQ or personality, an ethical watchdog in the UK has warned.
		It may soon be possible to choose children with a particular behavioural trait, according to the Nuffield Council on Bioethics.
		Currently, the selection of embryos using pre-implantation genetic diagnosis is restricted to serious diseases.
	news.bbc.co.uk /1/hi/health/2290020.stm (590 words)

	A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes -- Innan 100 (15): ...
		The selection intensity is estimated on the basis of
		The gene structures of the human RHCE and RHD genes (Upper) are according to refs.
		= 0.423 for the gene conversion parameter in exons 6–10
	www.pnas.org /cgi/content/full/100/15/8793 (3387 words)

	Polymorphism and intracellular self/not-self discrimination (Site not responding. Last check: 2007-10-20)
		A gene can be described as highly polymorphic if there are many sets of such alleles in the population.
		Thus, a cancer attributed to a mutation in an oncogene encoding A in one individual (A to A’) may be attacked immunologically with respect to a particular set of antigens (corresponding to genes encoding B, C and D).
		In view of the widespread evolutionary conservation of HSP genes, it was suggested that HSPs might have constituted a prototypic system for the processing of peptides, which evolved into the contemporary MHC-peptide system.
	mail.queensu.ca /~forsdyke/theorimm2.htm (5288 words)

	Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects -- Burke et al. 8 (3): 276 -- ...
		The green regions of subgroup 2 are identical to subgroup 1 sequences, and the blue region of subgroup 2 diverges.
		If one were to seek cancer-specific genes by looking at the original UniGene index cluster, the level of specificity to cancer libraries would only be ~53% = (100 × 9/17)%; however, at the subcluster level, the specificity level is 100%.
		Toward the development of a gene index to the human genome: An assessment of the nature of high-throughput EST sequence data.
	www.genome.org /cgi/content/full/8/3/276 (5659 words)

	JAEGER, SENGUPTA, RUZZO: Improved Gene Selection For Classification Of Microarrays (PSB 2003) (Site not responding. Last check: 2007-10-20)
		Genes of interest are typically selected by ranking genes according to a test-statistic and then choosing the top k genes.
		A problem with this approach is that many of these genes are highly correlated.
		We show that this filtered set of genes can be used to significantly improve existing classifiers.
	www.cs.washington.edu /homes/ruzzo/papers/jsr.html (149 words)

	GO Bibliography (Site not responding. Last check: 2007-10-20)
		Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.
		Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii.
		Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation.
	www.geneontology.org /GO.biblio.html (8841 words)

	Evidence for a Period of Directional Selection Following Gene Duplication in a Neurally Expressed Locus of ...
		gene duplication event early in the evolution of bony fishes.
		selection was involved in the functional divergence of the neural
		In the absence of selective pressure, the ratio of observed
	www.genetics.org /cgi/content/full/159/2/689 (5455 words)

	Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of ...
		Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
		selects a subset of predictive genes jointly for sample classification
		and stability of gene selection/sample classification to the
	bioinformatics.oupjournals.org /cgi/content/abstract/17/12/1131 (191 words)

	Statistical Characterization of Spervised Learning and Gene Selection Algorithms for Gene Expression Analysis (Site not responding. Last check: 2007-10-20)
		Advanced informatics for gene expression profiling is critically important for cancer diagnosis and treatment.
		The supervised learning technique, in particular, is a powerful tool for cancer-class prediction, and a feature selection technique is needed to identify marker genes for this prediction.
		Although an appropriate algorithm for dealing with the problem should be chosen from the various proposed supervised learning and gene selection methods, a guideline for the choice of method has yet to be established.
	www.iscb.org /ismb2003/posters/maedaATcslab.kecl.ntt.co.jp_350.html (125 words)

	INTRODUCTION: THE NATURE OF SCIENCE AND BIOLOGY
		While there have been some changes to the theory since 1859, most notably the incorporation of genetics and DNA into what is termed the "Modern Synthesis" during the 1940's, most scientists today accept evolution as the guiding theory on which modern biology is based.
		Define natural selection and briefly describe what is occurring when a population is said to evolve.
		The molecule that is the phsical carrier of inheritance is known as ___.
	www.estrellamountain.edu /faculty/farabee/BIOBK/BioBookintro.html (5361 words)

	Statistics.com Courses: Exploration and Analysis of DNA Microarray Data (Site not responding. Last check: 2007-10-20)
		The emergence of this technology has empowered researchers in functional genomics to monitor gene expression profiles, thousands of genes (perhaps even an entire genome) at a time.
		Suppose that a scientist wishes to know which genes were differentially expressed in several different types of cells.
		A DNA microarray for this experiment would be a tiny glass slide on which several genes of known sequence had been printed in a rectangular array of spots, one gene per spot.
	www.statistics.com /content/courses/microarray/index.html (1269 words)

	NCTR Scientific Publication List
		Chen, D., Chen, J.J. and Soong, S., Probe Rank Approaches for Gene Selection in Oligonucleotide Arrays with a Small Number of Replicates, Bioinformatics.
		Dobrovolsky, V.N., Bowyer, J.F., Pabarcus, M.K., Heflich, R.H., Bergquist, J., Williams, L.D., Doerge, D.R. and Casida, J.E., Effect of arylformamidase (kynurenine formamidase) gene inactivation in mice on enzymatic activity, kynurenine pathway metabolites and phenotype, BBA.
		Akerman, G.S., Rosenzweig, B., Domon, O.E., Tsai, C., Bishop, M.E., McGarrity, L.J., MacGregor, J.T., Sistare, F., Chen, J.J. and Morris, S.M., Alterations in gene expression profiles and the DNA damage response in ionizing radiation-exposedTK6 cells, Environmental and Molecular Mutagenesis.
	www.fda.gov /nctr/science/publications.html (2558 words)

	InvivoGen: Delivering Genes
		For more information on this service, click here.
		Fast-Media®, the fastest and easiest way to prepare E. coli selection media by using a microwave.
		pVITRO and pVIVO, dual promoter plasmids designed to co-express two genes of interest in vitro and in vivo.
	www.invivogen.com (112 words)

	Xiaole Shirley Liu
		We are interested in an integrated approach for bacteria operon prediction; motif identification for key transcription factors regulating gene expression and physiological changes (e.g.
		We are interested in using better statistical models, better gene selection (e.g.
		BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.
	genome.dfci.harvard.edu /xsliu (575 words)

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