Location of Repository

Integration of gene expression data with prior knowledge for network analysis and validation

By Michael Ante, Edgar Wingender and Mathias Fuchs
Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3298547
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles



    1. (1992). A survey of exact inference for contingency tables.
    2. (2002). An anatomy of normal and malignant gene expression.
    3. (1999). Berk BC: Fyn and JAK2 Mediate Ras Activation by Reactive Oxygen Species.
    4. (2004). Biological robustness. Nat Rev Genet
    5. (2006). C: Bcl-2 is a prognostic marker in breast cancer independently of the Nottingham Prognostic Index. Clin Cancer Res
    6. (2005). Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet
    7. (2009). Comparative Analysis Of Topological Patterns In Different Mammalian Networks. Genome Inf. Ser
    8. (2008). E: The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks.
    9. (2008). Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. Bioinformatics
    10. (2007). Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models. BMC Sys Biol
    11. (2006). From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res
    12. (2007). GD: Integration of biological networks and gene expression data using Cytoscape. Nat Protocols
    13. (1997). General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol
    14. (2000). Genetic network inference: from coexpression clustering to reverse engineering. Bioinformatics
    15. (2006). GK: Aurora Kinases: New Targets for Cancer Therapy. Clin Cancer Res
    16. (2004). Hogenesch JB: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA
    17. (2010). Kunkel LM: High-Density Genomewide Linkage Analysis of Exceptional Human Longevity Identifies Multiple Novel Loci. PLoS ONE
    18. (2005). Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA
    19. (2003). Miyano S: Inferring gene networks from time series microarray data using dynamic Bayesian networks.
    20. (2005). Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics
    21. (2008). Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. Bioinformatics
    22. (2007). Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge.
    23. (1999). Ribosomal S6 kinase (RSK1) activation requires signals dependent on and independent of the MAP kinase ERK. Current Biology
    24. (1960). Robust tests for equality of variances
    25. (2005). S: SH2-containing 5’-inositol phosphatase, SHIP2, regulates cytoskeleton organization and ligand-dependent downregulation of the epidermal growth factor.
    26. (2003). SA: Global functional profiling of gene expression. Genomics
    27. (2002). SA: Profiling Gene Expression Using Onto-Express. Genomics
    28. (2008). Sampling methods for Wallenius’ and Fisher’s noncentral hypergeometric distributions.
    29. (2004). Sparse graphical models for exploring gene expression data. J Multivariate Anal
    30. (2008). Speed TP: Network inference using informative priors.
    31. (2002). The Ceramide-centric universe of lipid-mediated cell regulation: stress encounters of the lipid kind.
    32. (2009). UA: Tissue-specific regulatory network extractor (TSREX): a database and software resource for the tissue and cell typespecific investigation of transcription factor-gene networks.
    33. (2003). Wattenberg BW: Activation of sphingosine kinase 1 by ERK1/2-mediated phosphorylation.
    34. (2004). WB: Phosphorylation of NG2 Proteoglycan by Protein Kinase C-α Regulates Polarized Membrane Distribution and Cell Motility.
    35. (2004). Wingender E: Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform
    36. (2008). Wingender E: ExPlain™: finding upstream drug targets in disease gene regulatory networks.
    37. (2005). Wingender E: Topology of mammalian transcription networks. Genome Inform
    38. (2006). Wingender E: TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res
    39. (2001). Yekutieli D: The Control of the False Discovery Rate in Multiple Testing under Dependency. The Annals of Statistics

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.