Matrix eQTL: Ultra fast eQTL analysis via large matrix operations

Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex diseases such as cancer, diabetes, and cystic fibrosis. A modern eQTL dataset contains millions of SNPs and thousands of transcripts measured for hundreds of samples. This makes the analysis computationally complex as it involves independent testing for association for every transcript-SNP pair. The heavy computational burden makes eQTL analysis less popular, often forces analysts to restrict their attention to just a subset of transcripts and SNPs. As larger genotype and gene expression datasets become available, the demand for fast tools for eQTL analysis increases. We present a new method for fast eQTL analysis via linear models, called Matrix eQTL. Matrix eQTL can model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors. In our experiment on large datasets Matrix eQTL was thousands of times faster than the existing popular software for QTL/eQTL analysis. Matrix eQTL is implemented as both Matlab and R packages and thus can easily be run on Windows, Mac OS, and Linux systems. The software is freely available at the following address: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTLComment: 9 pages, 1 figur

Final state interaction in K→2πK\to 2\pi decay

Contrary to wide-spread opinion that the final state interaction (FSI) enhances the amplitude $$, we argue that FSI does not increase the absolute value of this amplitude.Comment: 9 page

Existence of \sigma(600)/\kappa(900)-Particle and New Chiral Scalar Nonet ``Chiralons''

The \sigma(600) and \kappa(900), observed in the phase shift analyses, satisfy rather well the mass and width relation predicted by the SU(3)LsM and the SU(3)LsM with the vector and axial-vector meson nonets, and deserve to be the members of scalar \sigma-nonet, together with the observed resonances a_0(980) and f_0(980), as a chiral partner of pseudoscalar \pi-nonet. In the phase shift analyses an introduction of repulsive background phase \delta_{BG} is essential, whose origin has a close connection to the \lambda\phi^4 interaction in LsM. It is argued that the members of this \sigma-nonet, "Chiralons", have different properties and should be discriminated from the conventional ^3P_0-qqbar-scalar nonet.Comment: Talk at HADRON'97, the 7th int. conf. on hadron spectroscopy, BNL, August 1997. 4 pages with 1 eps figur

Loop-Less Electric Dipole Moment of the Nucleon in the Standard Model

We point out that the electric dipole moment of the neutron in the Standard Model is generated already at tree level to the second order in the weak interactions due to bound-state effects, without short-distance Penguin loops. The related contribution has a regular nonvanishing chiral limit and does not depend on the mass splitting between s and d quarks. We estimate it to be roughly 10^(-31)e*cm and expect a more accurate evaluation in the future. We comment on the connection between d_n and the direct CP-violation in D decays.Comment: 10 pages, 2 figure

Discrete Symmetries on the Light Front and a General Relation Connecting Nucleon Electric Dipole and Anomalous Magnetic Moments

We consider the electric dipole form factor, F_3(q^2), as well as the Dirac and Pauli form factors, F_1(q^2) and F_2(q^2), of the nucleon in the light-front formalism. We derive an exact formula for F_3(q^2) to complement those known for F_1(q^2) and F_2(q^2). We derive the light-front representation of the discrete symmetry transformations and show that time-reversal- and parity-odd effects are captured by phases in the light-front wave functions. We thus determine that the contributions to F_2(q^2) and F_3(q^2), Fock state by Fock state, are related, independent of the fundamental mechanism through which CP violation is generated. Our relation is not specific to the nucleon, but, rather, is true of spin-1/2 systems in general, be they lepton or baryon. The empirical values of the anomalous magnetic moments, in concert with empirical bounds on the associated electric dipole moments, can better constrain theories of CP violation. In particular, we find that the neutron and proton electric dipole moments echo the isospin structure of the anomalous magnetic moments, kappa^n ~ - kappa^p.Comment: 25 pages, 1 figure. Published version. Ref. adde

CP violation in K±→π0π0π±K^{\pm}\to\pi^0\pi^0\pi^{\pm} decay

CP violation leads to a difference between the parameters $g^+$ and $g^-$ describing the energy distributions of the charged pions produced in the $K^+ \to\pi^0 \pi^0 \pi^+$ and $K^- \to \pi^0\pi^0 \pi^-$ decays. We study the difference $(g^+ - g^-)$ as a function of the relative contributions from the QCD-penguin and the electroweak-penguin diagrams. We find that the combination of these contributions in $(g^+ - g^-)$ is very similar to the corresponding one defining the parameter $\epsilon'$ in the $K_L \to 2\pi$ decays. This observation allows a determination of the value of $(g^+ - g^-)$, using data on $\epsilon'$