Mohamed Elati

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We used the normalised data set available at http://genome-www.stanford.edu/cellcycle/data/ rawdata/combined.txt. This expression data set [9] comes from yeast cultures synchronised by four independent methods: alpha for alpha factor arrest, elu for elutriation, cdc15 for arrest of a cdc15 temperature-sensitive mutant, cdc28 for arrest of a cdc28(More)
MOTIVATION One of the most challenging tasks in the post-genomic era is the reconstruction of transcriptional regulation networks. The goal is to identify, for each gene expressed in a particular cellular context, the regulators affecting its transcription, and the co-ordination of several regulators in specific types of regulation. DNA microarrays can be(More)
Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may(More)
BACKGROUND Identifying gene functional modules is an important step towards elucidating gene functions at a global scale. Clustering algorithms mostly rely on co-expression of genes, that is group together genes having similar expression profiles. RESULTS We propose to cluster genes by co-regulation rather than by co-expression. We therefore present an(More)
UNLABELLED CoRegNet is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, CoRegNet can be used to: reconstruct a large-scale co-regulatory network, integrate regulation evidences such as transcription factor binding sites and ChIP data, estimate sample-specific(More)
UNLABELLED We introduce Pepper (Protein complex Expansion using Protein-Protein intERactions), a Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the(More)
In tumoral cells, gene regulation mechanisms are severely altered. Genes that do not react normally to their regulators' activity can provide explanations for the tumoral behavior, and be characteristic of cancer subtypes. We thus propose a statistical methodology to identify the misregulated genes given a reference network and gene expression data. Our(More)