Exact Properties of Some Exact Test Statistics for Comparing Two Binomial Proportions

Storer, Barry E.; Kim, Choongrak

doi:10.1080/01621459.1990.10475318

Cited by 124 publications

(88 citation statements)

References 10 publications

(15 reference statements)

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“…Read counts for each of the remaining SNPs were generated and imported into R (www.r-project.org) to test for allelic expression differences, using a Storer-Kim test (43) and previously established cutoff thresholds (11), following a suggested protocol to identify allele-specific expression (11,44,45). The Storer-Kim test was used to test the null hypothesis (h o : p1 -p2 = 0) in individuals with active ovaries and inactive ovaries separately, where p1 is defined as the proportion of Africanized reads in ExA individuals and p2 is defined as the proportion of Africanized reads in AxE individuals.…”

Section: Methodsmentioning

confidence: 99%

Testing the kinship theory of intragenomic conflict in honey bees ( Apis mellifera )

Galbraith

Kocher

Glenn³

et al. 2016

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

184

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Sexual reproduction brings genes from two parents (matrigenes and patrigenes) together into one individual. These genes, despite being unrelated, should show nearly perfect cooperation because each gains equally through the production of offspring. However, an individual's matrigenes and patrigenes can have different probabilities of being present in other relatives, so kin selection could act on them differently. Such intragenomic conflict could be implemented by partial or complete silencing (imprinting) of an allele by one of the parents. Evidence supporting this theory is seen in offspring-mother interactions, with patrigenes favoring acquisition of more of the mother's resources if some of the costs fall on half-siblings who do not share the patrigene. The kinship theory of intragenomic conflict is little tested in other contexts, but it predicts that matrigene-patrigene conflict may be rife in social insects. We tested the hypothesis that honey bee worker reproduction is promoted more by patrigenes than matrigenes by comparing across nine reciprocal crosses of two distinct genetic stocks. As predicted, hybrid workers show reproductive trait characteristics of their paternal stock, (indicating enhanced activity of the patrigenes on these traits), greater patrigenic than matrigenic expression, and significantly increased patrigenic-biased expression in reproductive workers. These results support both the general prediction that matrigene-patrigene conflict occurs in social insects and the specific prediction that honey bee worker reproduction is driven more by patrigenes. The success of these predictions suggests that intragenomic conflict may occur in many contexts where matrigenes and patrigenes have different relatednesses to affected kin. kinship theory | intragenomic conflict | evolutionary biology | social insects | sociogenomics

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Section: Methodsmentioning

confidence: 99%

Testing the kinship theory of intragenomic conflict in honey bees ( Apis mellifera )

Galbraith

Kocher

Glenn³

et al. 2016

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

184

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show abstract

“…Therefore, we could detect significant DAE between the two reciprocal F1 crosses (parent-of-origin effect) by rejecting the null hypothesis p 1 ¼ p 2 . Chi-squared test or Fisher's exact test could be used, but the Storer-Kim test has more power when the four counts are smaller (Storer and Kim, 1990). But the chi-squared or Storer-Kim test alone should not be relied on, because application of these tests shows a clear inflation of chi-squared statistics, indicating a consistent (Wang et al, 2013b).…”

Section: Estimation Of the Dae Ratio At Informative Snp Positions Andmentioning

confidence: 99%

Using next-generation RNA sequencing to identify imprinted genes

2014

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Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.

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“…The question that naturally arises is, is the multiplicity probability p A of system A similar to p B of system B? As in the case of binomial confidence intervals, there are several tests available in the literature (see Storer & Kim [1990] for a review). A conservative ''exact'' hypothesis test is based on Fisher (1935), where the hypothesis that p A ¼ p B is tested.…”

Section: B2 Comparing Binomial Distributionsmentioning

confidence: 99%

Deficit of Wide Binaries in the η Chamaeleontis Young Cluster

Brandeker

Jayawardhana

Khavari

et al. 2006

ApJ

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We have carried out a sensitive high-resolution imaging survey of stars in the young (6Y8 Myr), nearby (97 pc) compact cluster around Chamaeleontis to search for stellar and substellar companions. Our data were obtained using the NACO adaptive optics system on the ESO Very Large Telescope (VLT). Given its youth and proximity, any substellar companions are expected to be luminous, especially in the near-infrared, and thus easier to detect next to their parent stars. Here, we present VLT NACO adaptive optics imaging with companion detection limits for 17 Cha cluster members, and follow-up VLT ISAAC near-infrared spectroscopy for companion candidates. The widest binary detected is $0B2, corresponding to the projected separation 20 AU, despite our survey being sensitive down to substellar companions outside 0B3, and planetary-mass objects outside 0B5. This implies that the stellar companion probability outside 0B3 and the brown dwarf companion probability outside 0B5 are less than 0.16 with 95% confidence. We compare the wide binary frequency of Cha to that of the similarly aged TW Hydrae association and estimate the statistical likelihood that the wide binary probability is equal in both groups to be less than 2 ; 10 À4 . Even though the Cha cluster is relatively dense, stellar encounters in its present configuration cannot account for the relative deficit of wide binaries. We thus conclude that the difference in wide binary probability in these two groups provides strong evidence for multiplicity properties being dependent on environment. In two appendices we derive the projected separation probability distribution for binaries, used to constrain physical separations from observed projected separations, and summarize statistical tools useful for multiplicity studies.

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Exact Properties of Some Exact Test Statistics for Comparing Two Binomial Proportions

Cited by 124 publications

References 10 publications

Testing the kinship theory of intragenomic conflict in honey bees ( Apis mellifera )

Testing the kinship theory of intragenomic conflict in honey bees ( Apis mellifera )

Using next-generation RNA sequencing to identify imprinted genes

Deficit of Wide Binaries in the η Chamaeleontis Young Cluster

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