Principal component tests: applied to temporal gene expression data

Clustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical significance testing between the clusters can be meaningful in helping the researchers to assess if the classification results from implementing a clustering algorithm need to be improved, even after the cluster number has been determined by a well-established criterion. This is important when we want to identify highly-specific patterns through classification. We proposed to use a principal component (PC) test, which is an implementation of an exact F statistic for the measures at multiple endpoints based on elliptical distribution theory, to assess the statistical significance between clusters. A challenge in the implementation is the choice of the number (q) of principal components to be considered, which can severely influence the statistical power of the method. We optimized the determination via validation according to a permutation test based on the clustering to be evaluated. The method was applied to a public dataset in classifying genes according to their temporal gene expression profiles. The results demonstrated that the PC testing were useful for determining the optimal number of clusters.https://doi.org/10.1186/1471-2105-10-S1-S2

Transient Simulation on Dynamic Response of Liquid Annular Seals

Transient change of the operating parameters has a serious influence on the stability of liquid annular seals. Take the liquid annular seals as a research object, a numerical method based on six-degree-of-freedom (6DOF) to analyze the dynamic response of liquid annular seals under gravity impact load. The variations of the force of liquid seal and pressure as well as the axis trajectory in time history are investigated. The influence of different sealing clearance, different liquid viscosity and different rotor speed is also studied. The results show that the maximum sealing pressure and sealing force of gravity direction will increase greatly in a very short time and then reduce rapidly. When sealing clearance increases, the displacement response amplitudes of axis trajectory, the maximum sealing force of gravity direction and maximum sealing pressure also increase. When liquid viscosity increases, the displacement response am plitudes of axis trajectory, the maximum sealing force of gravity direction and maximum sealing pressure decrease. We also found that different rotor speed has almost no influence on the maximum sealing force of gravity direction and maximum sealing pressure

Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster

Predictive classification on the base of gene expression profiles appeared recently as an attractive strategy for identifying the biological functions of genes. Gene Ontology (GO) provides a valuable source of knowledge for model training and validation. The increasing collection of microarray data represents a valuable source for generating functional hypotheses of uncharacterized genes. This study focused on using support vector machines (SVM) to predict GO biological processes from individual or multiple-tissue transcriptional profiles of aging in Drosophila melanogaster. Ten-fold cross validation was implemented to evaluate the prediction. One-tail Fisher's exact test was conducted on each cross validation and multiple testing was addressed using BH FDR procedure. The results showed that, of the 148 pursued GO biological processes, fifteen terms each had at least one model with FDR-adjusted p-value (Adj.p) <0.05 and six had the values between 0.05 and 0.25. Furthermore, all these models had the prediction sensitivity (SN) over 30% and specificity (SP) over 80%. We proposed the concept of term-tissue specific models indicating the fact that the major part of the optimized prediction models was trained from individual tissue data. Furthermore, we observed that the memberships of the genes involved in all the three pursued children biological processes on mitochondrial electron transport could be predicted from the transcriptional profiles of aging (Adj.p < 0.01). This finding may be important in biology because the genes of mitochondria play a critical role in the longevity of C. elegans and D. melanogaster.https://doi.org/10.1186/1471-2105-9-12

Agrobacterium rhizogenes-mediated transformation of Superroot-derived Lotus corniculatus plants: a valuable tool for functional genomics

<p>Abstract</p> <p>Background</p> <p>Transgenic approaches provide a powerful tool for gene function investigations in plants. However, some legumes are still recalcitrant to current transformation technologies, limiting the extent to which functional genomic studies can be performed on. <it>Superroo</it>t of <it>Lotus corniculatus </it>is a continuous root cloning system allowing direct somatic embryogenesis and mass regeneration of plants. Recently, a technique to obtain transgenic <it>L. corniculatus </it>plants from <it>Superroot</it>-derived leaves through <it>A. tumefaciens-</it>mediated transformation was described. However, transformation efficiency was low and it took about six months from gene transfer to PCR identification.</p> <p>Results</p> <p>In the present study, we developed an <it>A. rhizogenes</it>-mediated transformation of <it>Superroot</it>-derived <it>L. corniculatus </it>for gene function investigation, combining the efficient <it>A. rhizogenes</it>-mediated transformation and the rapid regeneration system of <it>Superroot</it>. The transformation system using <it>A. rhizogenes </it>K599 harbouring pGFPGUS<it>Plus </it>was improved by validating some parameters which may influence the transformation frequency. Using stem sections with one node as explants, a 2-day pre-culture of explants, infection with K599 at OD₆₀₀= 0.6, and co-cultivation on medium (pH 5.4) at 22°C for 2 days enhanced the transformation frequency significantly. As proof of concept, <it>Superroot</it>-derived <it>L. corniculatus </it>was transformed with a gene from wheat encoding an Na⁺/H⁺antiporter (<it>TaNHX2</it>) using the described system. Transgenic <it>Superroot </it>plants were obtained and had increased salt tolerance, as expected from the expression of <it>TaNHX2</it>.</p> <p>Conclusion</p> <p>A rapid and efficient tool for gene function investigation in <it>L. corniculatus </it>was developed, combining the simplicity and high efficiency of the <it>Superroot </it>regeneration system and the availability of <it>A. rhizogenes</it>-mediated transformation. This system was improved by validating some parameters influencing the transformation frequency, which could reach 92% based on GUS detection. The combination of the highly efficient transformation and the regeneration system of <it>Superroot </it>provides a valuable tool for functional genomics studies in <it>L. corniculatus</it>.</p

Prediction of Tropical Cyclones’ Characteristic Factors on Hainan Island Using Data Mining Technology

A new methodology combining data mining technology with statistical methods is proposed for the prediction of tropical cyclones’ characteristic factors which contain latitude, longitude, the lowest center pressure, and wind speed. In the proposed method, the best track datasets in the years 1949~2012 are used for prediction. Using the method, effective criterions are formed to judge whether tropical cyclones land on Hainan Island or not. The highest probability of accurate judgment can reach above 79%. With regard to TCs which are judged to land on Hainan Island, related prediction equations are established to effectively predict their characteristic factors. Results show that the average distance error is improved compared with the National Meteorological Centre of China

STAT3 potentiates RNA polymerase I-directed transcription and tumor growth by activating RPA34 expression

Background: Deregulation of either RNA polymerase I (Pol I)-directed transcription or expression of signal transducer and activator of transcription 3 (STAT3) correlates closely with tumorigenesis. However, the connection between STAT3 and Pol I-directed transcription hasn’t been investigated. Methods: The role of STAT3 in Pol I-directed transcription was determined using combined techniques. The regulation of tumor cell growth mediated by STAT3 and Pol I products was analyzed in vitro and in vivo. RNAseq, ChIP assays and rescue assays were used to uncover the mechanism of Pol I transcription mediated by STAT3. Results: STAT3 expression positively correlates with Pol I product levels and cancer cell growth. The inhibition of STAT3 or Pol I products suppresses cell growth. Mechanistically, STAT3 activates Pol I-directed transcription by enhancing the recruitment of the Pol I transcription machinery to the rDNA promoter. STAT3 directly activates Rpa34 gene transcription by binding to the RPA34 promoter, which enhances the occupancies of the Pol II transcription machinery factors at this promoter. Cancer patients with RPA34 high expression lead to poor survival probability and short survival time. Conclusion: STAT3 potentiates Pol I-dependent transcription and tumor cell growth by activating RPA34 in vitro and in vivo