Extracting gene networks for low-dose radiation using graph theoretical algorithms.
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ABSTRACT:
SUBMITTER: Voy BH
PROVIDER: S-EPMC1513268 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documented, the detrimental effects of LDIR is not well understood and has been a topic of much debate. Since little is known about the effects of LDIR, various kinds of wet-lab and computational analyses are required to advance knowledge in this domain. In this paper we carry out an "upside-down pyramid" form of systems biology analysis of microarray data. We characterised the global genomic response following 10 cGy (low dose) and 100 cGy (high dose) doses of X-ray ionising radiation at four time points by analysing the topology of gene coexpression networks. This study includes a rich experimental design and state-of-the-art computational systems biology methods of analysis to study the differences in the transcriptional response of skin cells exposed to low and high doses of radiation.ResultsUsing this method we found important genes that have been linked to immune response, cell survival and apoptosis. Furthermore, we also were able to identify genes such as BRCA1, ABCA1, TNFRSF1B, MLLT11 that have been associated with various types of cancers. We were also able to detect many genes known to be associated with various medical conditions.ConclusionsOur method of applying network topological differences can aid in identifying the differences among similar (eg: radiation effect) yet very different biological conditions (eg: different dose and time) to generate testable hypotheses. This is the first study where a network level analysis was performed across two different radiation doses at various time points, thereby illustrating changes in the cellular response over time.
| S-EPMC3443446 | biostudies-literature
Project description:There are 160,000 cancer patients worldwide treated with particle radiotherapy (RT). With the advent of proton, and high (H) charge (Z) and energy (E) HZE ionizing particle RT, the cardiovascular diseases risk estimates are uncertain. In addition, future deep space exploratory-type missions will expose humans to unknown but low doses of particle irradiation (IR). We examined molecular responses using transcriptome profiling in left ventricular murine cardiomyocytes isolated from mice that were exposed to 90 cGy, 1 GeV proton ((1)H) and 15 cGy, 1 GeV/nucleon iron ((56)Fe) over 28 days after exposure. Unsupervised clustering analysis of gene expression segregated samples according to the IR response and time after exposure, with (56)Fe-IR showing the greatest level of gene modulation. (1)H-IR showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses, and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Validation of the signal transduction network by protein analysis and gel shift assay showed that particle IR clearly regulates a long-lived signaling mechanism for ERK1/2, p38 MAPK signaling and identified NFATc4, GATA4, STAT3, and NF-?B as regulators of the response at specific time points. These data suggest that the molecular responses and gene expression to (56)Fe-IR in cardiomyocytes are unique and long-lasting. Our study may have significant implications for the efforts of National Aeronautics and Space Administration to develop heart disease risk estimates for astronauts and for patients receiving conventional and particle RT via identification of specific HZE-IR molecular markers.
| S-EPMC4698384 | biostudies-literature
Project description:There is increasing interest in the potential of whole-brain computational models to provide mechanistic insights into resting-state brain networks. It is therefore important to determine the degree to which computational models reproduce the topological features of empirical functional brain networks. We used empirical connectivity data derived from diffusion spectrum and resting-state functional magnetic resonance imaging data from healthy individuals. Empirical and simulated functional networks, constrained by structural connectivity, were defined based on 66 brain anatomical regions (nodes). Simulated functional data were generated using the Kuramoto model in which each anatomical region acts as a phase oscillator. Network topology was studied using graph theory in the empirical and simulated data. The difference (relative error) between graph theory measures derived from empirical and simulated data was then estimated. We found that simulated data can be used with confidence to model graph measures of global network organization at different dynamic states and highlight the sensitive dependence of the solutions obtained in simulated data on the specified connection densities. This study provides a method for the quantitative evaluation and external validation of graph theory metrics derived from simulated data that can be used to inform future study designs.
| S-EPMC5312789 | biostudies-literature
Project description:ObjectiveFew studies have explored the clinical feasibility of using deep-learning reconstruction to reduce the radiation dose of CT. We aimed to compare the image quality and lung nodule detectability between chest CT using a quarter of the low dose (QLD) reconstructed with vendor-agnostic deep-learning image reconstruction (DLIR) and conventional low-dose (LD) CT reconstructed with iterative reconstruction (IR).Materials and methodsWe retrospectively collected 100 patients (median age, 61 years [IQR, 53-70 years]) who received LDCT using a dual-source scanner, where total radiation was split into a 1:3 ratio. QLD CT was generated using a quarter dose and reconstructed with DLIR (QLD-DLIR), while LDCT images were generated using a full dose and reconstructed with IR (LD-IR). Three thoracic radiologists reviewed subjective noise, spatial resolution, and overall image quality, and image noise was measured in five areas. The radiologists were also asked to detect all Lung-RADS category 3 or 4 nodules, and their performance was evaluated using area under the jackknife free-response receiver operating characteristic curve (AUFROC).ResultsThe median effective dose was 0.16 (IQR, 0.14-0.18) mSv for QLD CT and 0.65 (IQR, 0.57-0.71) mSv for LDCT. The radiologists' evaluations showed no significant differences in subjective noise (QLD-DLIR vs. LD-IR, lung-window setting; 3.23 ± 0.19 vs. 3.27 ± 0.22; P = .11), spatial resolution (3.14 ± 0.28 vs. 3.16 ± 0.27; P = .12), and overall image quality (3.14 ± 0.21 vs. 3.17 ± 0.17; P = .15). QLD-DLIR demonstrated lower measured noise than LD-IR in most areas (P < .001 for all). No significant difference was found between QLD-DLIR and LD-IR for the sensitivity (76.4% vs. 72.2%; P = .35) or the AUFROCs (0.77 vs. 0.78; P = .68) in detecting Lung-RADS category 3 or 4 nodules. Under a noninferiority limit of -0.1, QLD-DLIR showed noninferior detection performance (95% CI for AUFROC difference, -0.04 to 0.06).ConclusionQLD-DLIR images showed comparable image quality and noninferior nodule detectability relative to LD-IR images.
| S-EPMC10494344 | biostudies-literature
Project description:Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.
| S-EPMC5117560 | biostudies-literature
Project description:Identification of driver genes related to certain types of cancer is an important research topic. Several systems biology approaches have been suggested, in particular for the identification of breast cancer (BRCA) related genes. Such approaches usually rely on differential gene expression and/or mutational landscape data. In some cases interaction network data is also integrated to identify cancer-related modules computationally.We provide a framework for the comparative graph-theoretical analysis of networks integrating the relevant gene expression, mutations, and potein-protein interaction network data. The comparisons involve a graph-theoretical analysis of normal and tumor network pairs across all instances of a given set of breast cancer samples. The network measures under consideration are based on appropriate formulations of various centrality measures: betweenness, clustering coefficients, degree centrality, random walk distances, graph-theoretical distances, and Jaccard index centrality.Among all the studied centrality-based graph-theoretical properties, we show that a betweenness-based measure differentiates BRCA genes across all normal versus tumor network pairs, than the rest of the popular centrality-based measures. The AUROC and AUPR values of the gene lists ordered with respect to the measures under study as compared to NCBI BioSystems pathway and the COSMIC database of cancer genes are the largest with the betweenness-based differentiation, followed by the measure based on degree centrality. In order to test the robustness of the suggested measures in prioritizing cancer genes, we further tested the two most promising measures, those based on betweenness and degree centralities, on randomly rewired networks. We show that both measures are quite resilient to noise in the input interaction network. We also compared the same measures against a state-of-the-art alternative disease gene prioritization method, MUFFFINN. We show that both our graph-theoretical measures outperform MUFFINN prioritizations in terms of ROC and precions/recall analysis. Finally, we filter the ordered list of the best measure, the betweenness-based differentiation, via a maximum-weight independent set formulation and investigate the top 50 genes in regards to literature verification. We show that almost all genes in the list are verified by the breast cancer literature and three genes are presented as novel genes that may potentialy be BRCA-related but missing in literature.
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Project description:Dystonia, a debilitating neurological movement disorder, is characterized by involuntary muscle contractions and develops from a complex pathophysiology. Graph theoretical analysis approaches have been employed to investigate functional network changes in patients with different forms of dystonia. In this study, we aimed to characterize the abnormal brain connectivity underlying writer's cramp, a focal hand dystonia. To this end, we examined functional magnetic resonance scans of 20 writer's cramp patients (11 females/nine males) and 26 healthy controls (10 females/16 males) performing a sequential finger tapping task with their non-dominant (and for patients non-dystonic) hand. Functional connectivity matrices were used to determine group averaged brain networks. Our data suggest that in their neuronal network writer's cramp patients recruited fewer regions that were functionally more segregated. However, this did not impair the network's efficiency for information transfer. A hub analysis revealed alterations in communication patterns of the primary motor cortex, the thalamus and the cerebellum. As we did not observe any differences in motor outcome between groups, we assume that these network changes constitute compensatory rerouting within the patient network. In a secondary analysis, we compared patients with simple writer's cramp (only affecting the hand while writing) and those with complex writer's cramp (affecting the hand also during other fine motor tasks). We found abnormal cerebellar connectivity in the simple writer's cramp group, which was less prominent in complex writer's cramp. Our preliminary findings suggest that longitudinal research concerning cerebellar connectivity during WC progression could provide insight on early compensatory mechanisms in WC.
| S-EPMC8650489 | biostudies-literature
Project description:Graph analysis has become a popular approach to study structural brain networks in neurodegenerative disorders such as Alzheimer's disease (AD). However, reported results across similar studies are often not consistent. In this paper we investigated the stability of the graph analysis measures clustering, path length, global efficiency and transitivity in a cohort of AD (N = 293) and control subjects (N = 293). More specifically, we studied the effect that group size and composition, choice of neuroanatomical atlas, and choice of cortical measure (thickness or volume) have on binary and weighted network properties and relate them to the magnitude of the differences between groups of AD and control subjects. Our results showed that specific group composition heavily influenced the network properties, particularly for groups with less than 150 subjects. Weighted measures generally required fewer subjects to stabilize and all assessed measures showed robust significant differences, consistent across atlases and cortical measures. However, all these measures were driven by the average correlation strength, which implies a limitation of capturing more complex features in weighted networks. In binary graphs, significant differences were only found in the global efficiency and transitivity measures when using cortical thickness measures to define edges. The findings were consistent across the two atlases, but no differences were found when using cortical volumes. Our findings merits future investigations of weighted brain networks and suggest that cortical thickness measures should be preferred in future AD studies if using binary networks. Further, studying cortical networks in small cohorts should be complemented by analyzing smaller, subsampled groups to reduce the risk that findings are spurious.
| S-EPMC6072788 | biostudies-literature
Project description:Deep learning is one of the most advanced forms of machine learning. Most modern deep learning models are based on an artificial neural network, and benchmarking studies reveal that neural networks have produced results comparable to and in some cases superior to human experts. However, the generated neural networks are typically regarded as incomprehensible black-box models, which not only limits their applications, but also hinders testing and verifying. In this paper, we present an active learning framework to extract automata from neural network classifiers, which can help users to understand the classifiers. In more detail, we use Angluin's L* algorithm as a learner and the neural network under learning as an oracle, employing abstraction interpretation of the neural network for answering membership and equivalence queries. Our abstraction consists of value, symbol and word abstractions. The factors that may affect the abstraction are also discussed in the paper. We have implemented our approach in a prototype. To evaluate it, we have performed the prototype on a MNIST classifier and have identified that the abstraction with interval number 2 and block size 1 × 28 offers the best performance in terms of F1 score. We also have compared our extracted DFA against the DFAs learned via the passive learning algorithms provided in LearnLib and the experimental results show that our DFA gives a better performance on the MNIST dataset.
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Project description:Gene set analysis plays a critical role in the functional interpretation of omics data. Although this is typically done for one omics experiment at a time, there is an increasing need to combine gene set analysis results from multiple experiments performed on the same or different omics platforms, such as in multi-omics studies. Integrating results from multiple experiments is challenging, and annotation redundancy between gene sets further obscures clear conclusions. We propose to use a weighted set cover algorithm to reduce redundancy of gene sets identified in a single experiment. Next, we use affinity propagation to consolidate similar gene sets identified from multiple experiments into clusters and to automatically determine the most representative gene set for each cluster. Using three examples from over representation analysis and gene set enrichment analysis, we showed that weighted set cover outperformed a previously published set cover method and reduced the number of gene sets by 52-77%. Focusing on overlapping genes between the list of input genes and the enriched gene sets in over-representation analysis and leading-edge genes in gene set enrichment analysis further reduced the number of gene sets. A use case combining enrichment analysis results from RNA-Seq and proteomics data comparing basal and luminal A breast cancer samples highlighted the known difference in proliferation and DNA damage response. Finally, we used these algorithms for a pan-cancer survival analysis. Our analysis clearly revealed prognosis-related pathways common to multiple cancer types or specific to individual cancer types, as well as pathways associated with prognosis in different directions in different cancer types. We implemented these two algorithms in an R package, Sumer, which generates tables and static and interactive plots for exploration and publication. Sumer is publicly available at https://github.com/bzhanglab/sumer.
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