Metrics for GO based protein semantic similarity: a systematic evaluation

<p>Abstract</p> <p>Background</p> <p>Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best approach to semantic similarity in this context, since there is no conclusive evaluation of the various measures. Another issue, is whether electronic annotations should or not be used in semantic similarity calculations.</p> <p>Results</p> <p>We conducted a systematic evaluation of GO-based semantic similarity measures using the relationship with sequence similarity as a means to quantify their performance, and assessed the influence of electronic annotations by testing the measures in the presence and absence of these annotations. We verified that the relationship between semantic and sequence similarity is not linear, but can be well approximated by a rescaled Normal cumulative distribution function. Given that the majority of the semantic similarity measures capture an identical behaviour, but differ in resolution, we used the latter as the main criterion of evaluation.</p> <p>Conclusions</p> <p>This work has provided a basis for the comparison of several semantic similarity measures, and can aid researchers in choosing the most adequate measure for their work. We have found that the hybrid <it>simGIC</it> was the measure with the best overall performance, followed by Resnik's measure using a best-match average combination approach. We have also found that the average and maximum combination approaches are problematic since both are inherently influenced by the number of terms being combined. We suspect that there may be a direct influence of data circularity in the behaviour of the results including electronic annotations, as a result of functional inference from sequence similarity.</p

Finding New Genes for Non-Syndromic Hearing Loss through an In Silico Prioritization Study

At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL), but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score () that relies on the assumption that functionally related genes might contribute to the same (disease) phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value that the former pair-wise is greater than the latter, justifying a prioritization strategy based on the functional similarity of candidate genes respect to the disease gene set. A cross-validation test measured to what extent the ranking for NSHL is different from a random ordering: adding 15% of the disease genes to the candidate gene set, the ranking of the disease genes in the first eight positions resulted statistically different from a hypergeometric distribution with a p-value and a power. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations

Dokumentation der Energie und Massenstrombilanzierung für ADAM I im Online-Betrieb

The methanation process is of considerable importance to both the production of "Substitute Natural Gas" on the basis of coal gasification and the "Nuclear Long - Distance Energy System". The report describes how the data resulting from experiments with pilot plant ADAM I were recorded and integrated into a computer program. The experimental results are of use to the optimization of the methanation process within the "Nuclear Long-Distance Energy System.

EVA I : Versuch zur Kinetik der Methan-Dampfreformierung in einer Katalysatorschüttung

In an EVA I test run with a packed bed of raschig ring catalysts (GIRDLER G-56H) pressure,temperature and flow rate of the process gas were largely varied. Equations have been evaluated for the kinetics of methane and ethane steam reforming. Besides Arrhenius term and equilibrium stop the equation for the methane reforming reaction includes a term, which is dependent on the gas velocity and describes the influence of the diffusion barriers on the experimentally observed conversion

Wärmeübergang und Kinetik bei der Methan Reformierung mit H2_{2}O-CO2_{2} Gemischen in EVA I

The synthesis of alcohols requires a special synthesis gas, which cannot be produced by steam reforming of natural gas, as it was done in EVA I before. The required low H$_{2}$/C0 ratios down to 1 in the synthesis gas could be adjust by addition of CO$_{2}$ to the feed mixture of natural gas and steam. About half of the CO$_{2}$ is converted to CO by the shift reaction. The experimental heat transfer and kinetic data are in good agreement with correlations used for the reforming process without CO$_{2}$ addition