In search of functional association from time-series microarray data based on the change trend and level of gene expression

BACKGROUND: The increasing availability of time-series expression data opens up new possibilities to study functional linkages of genes. Present methods used to infer functional linkages between genes from expression data are mainly based on a point-to-point comparison. Change trends between consecutive time points in time-series data have been so far not well explored. RESULTS: In this work we present a new method based on extracting main features of the change trend and level of gene expression between consecutive time points. The method, termed as trend correlation (TC), includes two major steps: 1, calculating a maximal local alignment of change trend score by dynamic programming and a change trend correlation coefficient between the maximal matched change levels of each gene pair; 2, inferring relationships of gene pairs based on two statistical extraction procedures. The new method considers time shifts and inverted relationships in a similar way as the local clustering (LC) method but the latter is merely based on a point-to-point comparison. The TC method is demonstrated with data from yeast cell cycle and compared with the LC method and the widely used Pearson correlation coefficient (PCC) based clustering method. The biological significance of the gene pairs is examined with several large-scale yeast databases. Although the TC method predicts an overall lower number of gene pairs than the other two methods at a same p-value threshold, the additional number of gene pairs inferred by the TC method is considerable: e.g. 20.5% compared with the LC method and 49.6% with the PCC method for a p-value threshold of 2.7E-3. Moreover, the percentage of the inferred gene pairs consistent with databases by our method is generally higher than the LC method and similar to the PCC method. A significant number of the gene pairs only inferred by the TC method are process-identity or function-similarity pairs or have well-documented biological interactions, including 443 known protein interactions and some known cell cycle related regulatory interactions. It should be emphasized that the overlapping of gene pairs detected by the three methods is normally not very high, indicating a necessity of combining the different methods in search of functional association of genes from time-series data. For a p-value threshold of 1E-5 the percentage of process-identity and function-similarity gene pairs among the shared part of the three methods reaches 60.2% and 55.6% respectively, building a good basis for further experimental and functional study. Furthermore, the combined use of methods is important to infer more complete regulatory circuits and network as exemplified in this study. CONCLUSION: The TC method can significantly augment the current major methods to infer functional linkages and biological network and is well suitable for exploring temporal relationships of gene expression in time-series data

Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation

By combining information on the yeast transcription network and high-resolution time-series data with a series of factors, support is provided for the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control

Effect of dark matter on shadows and rings of a brane-world black hole illuminated by various accretions

In this paper, by taking the accretions into account, the observational shadows and rings casted by the Brane-world black hole are numerically investigated when the observer located at the cosmological horizon. The results here show that the radius $r_p$ of photon sphere increased with cosmological parameter $\alpha$ and dark matter parameter $\beta$, while the impact parameter $b_p$ decreased with $\alpha$ and increased with $\beta$. For the thin-disk accretion, it turns out that the total observed intensity are mainly composed of the direct emission, while lensing ring and photon ring only contribute a small contribution and a negligible contribution, respectively. And, we find that shadow and rings exhibit some different and interesting features when the disk located at different positions. For the static and infalling spherical accretions, it is obvious that the size of shadow is always the same for both accretions, which means that shadow is only related to the geometry of space time in this case. The luminosity of shadow and photon sphere are closely related to the Doppler effect and the emissivity per unit volume $j({\nu_e})$. In addition, the influence of dark matter and cosmological constant on observed intensity of shadows and rings are carefully emphasized throughout of this paper. Finally, we obtained the burring images of shadows and rings by using the nominal resolution of the Event Horizon Telescope, and studied the upper limits on the X-clod dark matter parameter $\beta$ with the aid of the data of the shadow of M87.Comment: 66figures, 4tables, 26pages,accepted by SCIENCE CHINA Physics, Mechanics & Astronomy,202

Potential super-hard Osmium di-nitride with fluorite structure: First-principles calculations

We have performed systematic first-principles calculations on di-carbide, -nitride, -oxide and -boride of platinum and osmium with the fluorite structure. It is found that only PtN$_{2}$, OsN$_{2}$ and OsO$_{2}$ are mechanically stable. In particular OsN$_{2}$ has the highest bulk modulus of 360.7 GPa. Both the band structure and density of states show that the new phase of OsN$_{2}$ is metallic. The high bulk modulus is owing to the strong covalent bonding between Os 5\textit{d} and N 2\textit{p} states and the dense packed fluorite structure.Comment: Phys. Rev. B 74,125118 (2006

Experimental Test of Bell inequalities with Six-Qubit Graph States

We report on the experimental realization of two different Bell inequality tests based on six-qubit linear-type and Y-shape graph states. For each of these states, the Bell inequalities tested are optimal in the sense that they provide the maximum violation among all Bell inequalities with stabilizing observables and possess the maximum resistance to noise.Comment: 4 pages, 2 figure

(E)-Ethyl 2-cyano-3-[4-(4,5-diphenyl-1H-imidazol-2-yl)phen­yl]acrylate dihydrate

In the title compound, C27H21N3O2·2H2O, the three benzene rings attached to the heterocyclic imidazole ring are not coplanar with the latter, making dihedral angles of 14.8 (2), 31.4 (2), and 37.5 (2)°, respectively, for the benzene ring planes in the 2-, 4- and 5-positions. In the crystal, there are two water mol­ecules which serve as connectors between the acrylate mol­ecules and stabilize the structure via N—H⋯O, O—H⋯N, C—H⋯O and O—H⋯O hydrogen bonding