Global modeling of transcriptional responses in interaction networks
@article{Lahti2010GlobalMO, title={Global modeling of transcriptional responses in interaction networks}, author={Leo Lahti and Juha E. A. Knuuttila and Samuel Kaski}, journal={Bioinformatics}, year={2010}, volume={26 21}, pages={ 2713-20 } }
MOTIVATION
Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues.
RESULTS
We introduce a novel…
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References
SHOWING 1-10 OF 72 REFERENCES
Discovering regulatory and signalling circuits in molecular interaction networks
- Computer Science, BiologyISMB
- 2002
This paper introduces an approach for screening a molecular interaction network to identify active subnetworks, i.e., connected regions of the network that show significant changes in expression over particular subsets of conditions.
Identification of functional modules using network topology and high-throughput data
- Biology, Computer ScienceBMC Systems Biology
- 2006
A novel algorithmic framework is described that can accurately identify functional modules and carries the promise to be highly useful in analysis of high throughput data.
Physiology, Pathology and Relatedness of Human Tissues from Gene Expression Meta-Analysis
- BiologyPloS one
- 2008
It is proposed that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods and some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.
- Biology, Computer ScienceProceedings of the National Academy of Sciences of the United States of America
- 2004
This work performs analysis of a highly diverse collection of genomewide data sets to reveal the modular organization of the yeast system, and uses the identified modules to study the yeast transcriptional network and predict the function of >800 uncharacterized genes.
Biological context networks: a mosaic view of the interactome
- BiologyMolecular systems biology
- 2006
This paper introduces a novel graph construct called a biological context network that explicitly captures changing patterns of interaction from one biological context to another, and shows that aggregating small process‐specific protein interaction sub‐networks leads to the emergence of observed scale‐free properties.
A genomic strategy to elucidate modules of oncogenic pathway signaling networks.
- BiologyMolecular cell
- 2009
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
- BiologyBMC Bioinformatics
- 2006
An algorithm is developed that detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs, and it is found that cMonkey biclusters are more parsimonious with all available evidence for co-regulation.
Gene set internal coherence in the context of functional profiling
- BiologyBMC Genomics
- 2008
Using a large collection of microarray data, a detailed survey of internal correlation in GO terms and KEGG pathways is carried out, providing a coherence index to be used for measuring functional module co-regulation.
Gene expression network analysis and applications to immunology
- Computer ScienceBioinform.
- 2007
A gene interaction network is constructed and search for high-scoring subnetworks and several improvements in terms of scoring functions and algorithms are made, resulting in higher speed and accuracy and easier biological interpretation.
A novel signaling pathway impact analysis
- BiologyBioinform.
- 2009
A novel signaling pathway impact analysis (SPIA) that combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition.