A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions

Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true motifs when noise is high and shows higher specificity for predicting the tissue-specific functions of CRRs

PHENIX Measurements of Higher-order Flow Harmonics for Identified Charged Hadrons in Au+Au collisions at sNN=39−200\sqrt{s_{NN}}=39-200 GeV

The azimuthal anisotropy coefficients $v_{2,3,4}$, characterizing collective flow in Au+Au collisions, are presented for identified particle species as a function of transverse momentum ($p_T$), centrality ($\rm{cent}$) and beam collision energy ($\sqrt{s_{NN}}=0.039-0.20$ TeV). The $v_n$ values for each particle species, show little, if any, change over the measured beam energy range, and ${v_n}/{(n_q)^{n/2}}$ vs. $KE_T/n_q$ scales to a single curve (constituent quark number ($n_q)$ scaling) for each $n$, over a broad range of transverse kinetic energies ($KE_T$). A comparison of $v_2(p_T)$ for individual particle species obtained in Au+Au collisions at $\sqrt{s_{NN}}=0.20$ TeV (RHIC) and Pb+Pb collisions at $\sqrt{s_{NN}}=2.76$ TeV (LHC), indicate stronger collective flow at the LHC. These flow measurements and their scaling patterns, can provide important additional constraints for extraction of the specific viscosity $\eta/s$.Comment: 4 pages, 5 figures, proceedings of talk at the 23rd International Conference on Ultra-Relativistic Nucleus-Nucleus Collisions, QM2012, August 13-18, 2012, Washington D