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Systematic prediction of novel gene targets associated to mitosis:

Systematic prediction of novel gene targets associated to mitosis:. Integration of prediction methods. Experimental validation. Novel s pindle proteins. Fisher. 1).

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Systematic prediction of novel gene targets associated to mitosis:

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  1. Systematicprediction of novel gene targets associatedto mitosis: Integration of predictionmethods Experimental validation Novel spindle proteins Fisher 1) Rojas et al. Uncoveringthe molecular machinery of the human spindle--anintegration of wet and drysystemsbiology. PLoSOne. 2012;7(3):e31813 Kernels Novel Chromos. Conden. Genes 2) Jean-KarimHériché et al. …& Jan Ellenberg. Integration of biological data by kernels on graph nodes allows prediction of genes involved in mitotic chromosome condensation . Submitted.

  2. Functionalprediction of novel genes and gene relationshipsrelatedtocellmigration: 3) Case study: ECM stiffnesseffectsin the MCF10CA1a malignanttumourcellline. Functionalsystemsprediction usingproteinnetworks and kernels Diferentiallyexpressed genes Transcriptomic and proteomic data In collaborationwithStaffanStrömblad.

  3. Methodstoidentifygeneticexpressionvariationassociatedwithdrug response in heterogeneoustumours 1) Tumourlines / taxoltreatment 4) Tumourlinesseparation: Sensitive / Resistant Gene expressionmatrix + Celltypesfrequencymatrix + Multi-regression 3) 2) Sensitive / Resistant Heatmap of theidentified genes Changes in expressiondependantoncelltypes and drugtreatment response In collaborationwithAltschuler & Wulab (UT Southwestern). Manuscript in preparation.

  4. Relationship of genes in differentontologies: Gene Ontology (GO) and experimental phenotypes. Metricstomeasuregene pairssimilarity in differentontologies: Metriccorrelationcomparisonstudies: Semanticsimilarity in GO. • Euclideandistance • StandarizedEuclideandistance • Mahalanobisdistance • City Block metric • Minkowskimetric • Cosinedistance • Correlationdistance • Hammingdistance • HammingModifiedsimilarity • Jaccarddistance • Clusteringdistance • Clusteringsimilarity • TF-IDF similarity Ongoingwork in collaborationwithGabriellaRustici.

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