Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

2016-04-01
Tunçbağ, Nurcan
KEDAIGLE, Amanda
Soltis, Anthony R.
GITTER, Anthony
FRAENKEL, Ernest
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
87
views
234
downloads
High-throughput, 'omic' methods provide sensitive measures of biological responses to per-turbations. However, inherent biases in high-throughput assays make it difficult to interpret experiments in which more than one type of data is collected. In this work, we introduce Omics Integrator, a software package that takes a variety of 'omic' data as input and identifies putative underlying molecular pathways. The approach applies advanced network optimization algorithms to a network of thousands ofmolecular interactions to find high-confidence, interpretable subnetworks that best explain the data. These subnetworks connect changes observed in gene expression, protein abundance or other global assays to proteins that may not have been measured in the screens due to inherent bias or noise in measurement. This approach reveals unannotated molecular pathways that would not be detectable by searching pathway databases. Omics Integrator also provides an elegant framework to incorporate not only positive data, but also negative evidence. Incorporating negative evidence allows Omics Integrator to avoid unexpressed genes and avoid being biased toward highly-studied hub proteins, except when they are strongly implicated by the data. The software is comprised of two individual tools, Garnet and Forest, that can be run together or independently to allow a user to perform advanced integration of multiple types of high-throughput data as well as create condition-specific subnetworks of protein interactions that best connect the observed changes in various datasets. It is available at http://fraenkel.mit.edu/omicsintegrator and on GitHub at https://github.com/fraenkel-lab/OmicsIntegrator.
Transcription factors, Protein interaction networks, Network analysis, Interaction networks, Integrators, DNA transcription
https://hdl.handle.net/11511/31590
PLOS COMPUTATIONAL BIOLOGY
Graduate School of Informatics, Article

Suggestions

Aromatic amino acid synthesis performance of bacillus acidocaldarius
Kocabaş, Pınar; Çalık, Pınar; Department of Chemical Engineering (2004)
In this study, the effects of bioprocess operation parameters on aromatic amino acid synthesis performance of Bacillus acidocaldarius were investigated. Firstly, in laboratory scale shake-bioreactors, a defined medium was designed in terms of its carbon and nitrogen sources, to achieve the highest cell concentration. Thereafter, the effects of bioprocess operation parameters, i.e., pH and temperature were investigated; and the optimum medium contained (kg m-3): fructose, 8; (NH4)2HPO4, 5; CaCl2, 0.2; KH2PO4...
Visualizing the protein-protein interactions network in virtual reality and mixed reality environments
Şenderin, Büşra; Sürer, Elif; Tunçbağ, Nurcan; Department of Modeling and Simulation (2021-8)
Protein-protein interactions (PPI) define the physical contact of two or more protein structures. When these interactions are combined, the protein-protein interaction network (PPIN) is formed. The interactions between protein structures are distinct interactions—they happen in specific binding locations on proteins, and they have a specific biological function that they take on. With these networks, the processes within a cell or a living organism when healthy or diseased can be studied. In this thesis, a ...
Integration of topological measures for eliminating non-specific interactions in protein interaction networks
BAYIR, Murat Ali; GUNEY, Tacettin Dogacan; Can, Tolga (Elsevier BV, 2009-05-28)
High-throughput protein interaction assays aim to provide a comprehensive list of interactions that govern the biological processes in a cell. These large-scale sets of interactions, represented as protein-protein interaction networks, are often analyzed by computational methods for detailed biological interpretation. However, as a result of the tradeoff between speed and accuracy, the interactions reported by high-throughput techniques occasionally include non-specific (i.e., false-positive) interactions. ...
Hplc-dad isolation of antioxidant compounds in aesculus hippocastanum bark extracts and cytotoxic effects on hl-60 cells
Özdoğan, Nizamettin; Özdoğan, Nizamettin; Department of Biochemistry (2007)
This study was designed to investigate the cytotoxic and antioxidative properties of Aesculus hippocastanum L. (A. hippocastanum) bark extracts. Dried and powdered barks were extracted in ethanol, methanol, water and ethylacetate at a ratio of 1:6 (w/v). Antioxidative capacity of each extract (ethanol, methanol, water and ethylacetate) were determined by their ability to scavenge 1, 1 -diphenyl-2-picryl-hydrazyl radical (DPPH). Effective concentration (EC50) values were calculated as 0.010 mg/mL 0.011 mg/mL...
LIFE SITUATIONS AND ATTITUDES OF THE TURKISH ELDERLY TOWARD INSTITUTIONAL LIVING WITHIN A CROSS-CULTURAL-PERSPECTIVE
IMAMOGLU, EO; İmamoğlu, Vacit (1992-03-01)
Based on the findings of a cross-cultural study, this paper aims (a) to explore changes in the current life situations and attitudes of the Turkish elderly toward institutional living in terms of age, sex, and urbanization; and (b) by way of comparison with the Swedish case, to assess the generalizability of the findings within a cross-cultural perspective. Indepth interviews were carried out with 448 Turkish males and females (55-71 years) residing in small towns, cities, and metropolitan areas. The comp...
Citation Formats
N. Tunçbağ, A. KEDAIGLE, A. R. Soltis, A. GITTER, and E. FRAENKEL, “Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package,” PLOS COMPUTATIONAL BIOLOGY, pp. 0–0, 2016, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/31590.
METU IIS - Integrated Information Service open@metu.edu.tr