188 research outputs found
Statistical data mining for symbol associations in genomic databases
A methodology is proposed to automatically detect significant symbol
associations in genomic databases. A new statistical test is proposed to assess
the significance of a group of symbols when found in several genesets of a
given database. Applied to symbol pairs, the thresholded p-values of the test
define a graph structure on the set of symbols. The cliques of that graph are
significant symbol associations, linked to a set of genesets where they can be
found. The method can be applied to any database, and is illustrated MSigDB C2
database. Many of the symbol associations detected in C2 or in non-specific
selections did correspond to already known interactions. On more specific
selections of C2, many previously unkown symbol associations have been
detected. These associations unveal new candidates for gene or protein
interactions, needing further investigation for biological evidence
Simultaneous growth of two cancer cell lines evidences variability in growth rates
Cancer cells co-cultured in vitro reveal unexpected differential growth rates
that classical exponential growth models cannot account for. Two
non-interacting cell lines were grown in the same culture, and counts of each
species were recorded at periodic times. The relative growth of population
ratios was found to depend on the initial proportion, in contradiction with the
traditional exponential growth model. The proposed explanation is the
variability of growth rates for clones inside the same cell line. This leads to
a log-quadratic growth model that provides both a theoretical explanation to
the phenomenon that was observed, and a better fit to our growth data
Simulation of Gene Regulatory Networks
This limited review is intended as an introduction to the fast growing subject of mathematical modelling of cell metabolism and its biochemical pathways, and more precisely on pathways linked to apoptosis of cancerous cells. Some basic mathematical models of chemical kinetics, with emphasis on stochastic models, are presented
Patterns in species richness and endemismof European freshwater fish
Aim
To analyse the patterns in species richness and endemism of the native
European riverine fish fauna, in the light of the Messinian salinity crisis and the Last
Glacial Maximum (LGM).
Location
European continent.
Methods
After gathering native fish faunistic lists of 406 hydrographical networks,
we defined large biogeographical regions with homogenous fish fauna, based on a
hierarchical cluster analysis. Then we analysed and compared the patterns in species
richness and endemism among these regions, as well as species–area relationships.
Results
Among the 233 native species present in the data set, the Cyprinidae family
was strongly dominant (> 50% of the total number of species). Seven biogeographical
regions were defined: Western Peri-Mediterranea, Central Peri-Mediterranea,
Eastern Peri-Mediterranea, Ponto-Caspian Europe, Northern Europe, Central Europe
and Western Europe. The highest regional species richness was observed for Central
Peri-Mediterranea and Ponto-Caspian Europe. The highest endemic richness was
found in Central Peri-Mediterranea. Species–area relationships were characterized by
high slope values for Peri-Mediterranean Europe and low values for Central and
Western Europe.
Main conclusions
The results were in agreement with the ‘Lago Mare’ hypothesis
explaining the specificity of Peri-Mediterranean fish fauna, as well as with the history
of recolonization of Central and Western Europe from Ponto-Caspian Europe
following the LGM. The results also agreed with the mechanisms of speciation and
extinction influencing fish diversity in hydrographical networks. We advise the use
of the seven biogeographical regions for further studies, and suggest considering
Peri-Mediterranean Europe and Ponto-Caspian Europe as ‘biodiversity hotspots’ for
European riverine fish
nwCompare and AutoCompare Softwares for Proteomics and Transcriptomics Data Mining – Application to the Exploration of Gene Expression Profiles of Aggressive Lymphomas
chapitre 22International audienc
Notes sur les phlébotomes de l'Aïr (Niger)
238 phlébotomes appartenant à 7 espèces ont été récoltés dans 4 stations du massif de l'Aïr au Niger. #Phlebotomus bergeroti était l'espèce dominante sur appât animal (âne) et dans les récoltes domiciliaires. Une attention spéciale est portée à #P. alexandri, vecteur de kala-azar dans d'autres foyers. (Résumé d'auteur
Variabilité à long terme des peuplements de poissons : résultats provenant de rivières françaises et ouest africaines
La variabilité à long terme de 18 peuplements de poissons a été étudiée dans des rivières françaises et ouest africaines. Les principaux résultats sont les suivants : 1) le coefficient de variation (CV) de la richesse spécifique, le CV de l'abondance totale et le CV moyen des espèces constitutives du peuplement augmentent avec la durée de l'étude; 2) selon la classification proposée par GROSSMAN et al. (1990) basée sur le CV moyen de l'abondance des espèces, tous les peuplements étudiés rentrent dans la catégorie des peuplements à fortes fluctuations interannuelles. Cependant certaines populations (les salmonidés en Bretagne par exemple) présentent une faible variabilité de leur densité; 3) dans le Rhône, les peuplements dont les populations manifestent une grande variabilité interannuelle sont ceux présentant le plus grand taux de renouvellement en espèces. Ce résultat est en accord avec l'hypothèse de HORWITZ (1978, "extermination hypothesis"). (Résumé d'auteur
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