Omic space: coordinate-based integration and analysis of genomic phenomic interactions

@article{Toyoda2004OmicSC,
  title={Omic space: coordinate-based integration and analysis of genomic phenomic interactions},
  author={Tetsuro Toyoda and Akiyoshi Wada},
  journal={Bioinformatics},
  year={2004},
  volume={20 11},
  pages={
          1759-65
        }
}
MOTIVATION With the recent progress in genomics, various data sets of omic interactions describing networks of omic elements have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of data sets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic… 

Figures and Tables from this paper

OmicBrowse: a browser of multidimensional omics annotations
TLDR
OmicBrowse displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms.
A study on multi-omic oscillations in Escherichia coli metabolic networks
TLDR
The integration of multi-omic data reveals that E.coli multi-omics metabolic networks contain position dependent and recurring patterns which could provide clues of long range correlations in the bacterial genome.
Multi-Omics Data-Driven Systems Biology of E. coli
TLDR
This study uncovered the complementary strategies of E. coli that result in a metabolic network robust against various types of perturbations, therefore demonstrating the power of a multi-omics, data-driven approach for understanding the functional principles of total cellular systems.
A flexible representation of omic knowledge for thorough analysis of microarray data
TLDR
A new insight is discovered that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress.
Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare
TLDR
There are big challenges in multi-omic data integration, modelling and systems-level analyses, particularly with the fast emerging HTO technologies, as well as existing and emerging systems genomics approaches.
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks
TLDR
A combined analysis of two diabetes-related traits suggests that molecular-level relationships such as the interaction among leptin receptor (Lepr), peroxisome proliferators-activated receptor-gamma (Pparg) and insulin receptor substrate 1 (Irs1), are candidate causal networks affecting the traits in a multigenic manner.
Bioinformatic Tools in Crop Improvement
TLDR
The review details recent advances in plant omics data acquisition sites, together with relevant databases and advance molecular technology under clear biological categories to enable the full potential of bioinformatics and use in crop improvement programs to be achieved.
Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse
TLDR
The immune response was the biologically most coherent signature that emerged from analyses among several other biological processes and corroborates other studies showing a strong immune response in patients less likely to relapse.
Genomics and Bioinformatics Resources for Crop Improvement
TLDR
A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity.
Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models.
TLDR
A statistical method is introduced that estimates the precise splicing points and the exon/intron structure of a structurally unknown gene by maximizing the odds or the ratio of posterior probabilities of the structure under the observation of array signal intensities and nucleic acid sequences.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 37 REFERENCES
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
TLDR
This paper provides the first global evidence that genes with similar expression profiles are more likely to encode interacting proteins, and shows how this correlation between transcriptome and interactome data can be used to improve the quality of hypotheses based on the information from both approaches.
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
TLDR
It is shown that a significant fraction of the protein-protein interactions in genome-wide datasets, as well as many of the individual interactions reported in the literature, are inconsistent with the known 3D structures of three recent complexes.
A comprehensive two-hybrid analysis to explore the yeast protein interactome
TLDR
The comprehensive analysis using a system to examine two-hybrid interactions in all possible combinations between the budding yeast Saccharomyces cerevisiae is completed and would significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.
Cluster analysis and display of genome-wide expression patterns.
TLDR
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
TLDR
Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
A bioinformatics-based strategy identifies c-Myc and Cdc25A as candidates for the Apmt mammary tumor latency modifiers.
TLDR
The data suggest that c-Myc and Cdc25A are Apmt1 and ApmT2, and suggest that, at least in certain instances, bioinformatics can be utilized to bypass congenic construction and subsequent mapping in conventional QTL studies.
The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.
TLDR
The development of a mammalian protein-protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks is described, which is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.
Genetics of gene expression surveyed in maize, mouse and man
Treating messenger RNA transcript abundances as quantitative traits and mapping gene expression quantitative trait loci for these traits has been pursued in gene-specific ways. Transcript abundances
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
TLDR
It is shown that proteins having matching or similar profiles strongly tend to be functionally linked, and this method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.
The large-scale organization of metabolic networks
TLDR
This analysis of metabolic networks of 43 organisms representing all three domains of life shows that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.
...
1
2
3
4
...