scholarly journals Graph Theoretic and Pearson Correlation-Based Discovery of Network Biomarkers for Cancer

Data ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 81 ◽  
Author(s):  
Raihanul Bari Tanvir ◽  
Tasmia Aqila ◽  
Mona Maharjan ◽  
Abdullah Al Mamun ◽  
Ananda Mohan Mondal
Keyword(s):  
Gene Network ◽  
Pearson Correlation ◽  
Maximal Clique ◽  
Bipartite Graphs ◽  
Graph Theoretic ◽  
Network Modules ◽  
Network Properties ◽  
Network Biomarkers ◽  
Highly Correlated ◽  
Disease Stages

Two graph theoretic concepts—clique and bipartite graphs—are explored to identify the network biomarkers for cancer at the gene network level. The rationale is that a group of genes work together by forming a cluster or a clique-like structures to initiate a cancer. After initiation, the disease signal goes to the next group of genes related to the second stage of a cancer, which can be represented as a bipartite graph. In other words, bipartite graphs represent the cross-talk among the genes between two disease stages. To prove this hypothesis, gene expression values for three cancers— breast invasive carcinoma (BRCA), colorectal adenocarcinoma (COAD) and glioblastoma multiforme (GBM)—are used for analysis. First, a co-expression gene network is generated with highly correlated gene pairs with a Pearson correlation coefficient ≥ 0.9. Second, clique structures of all sizes are isolated from the co-expression network. Then combining these cliques, three different biomarker modules are developed—maximal clique-like modules, 2-clique-1-bipartite modules, and 3-clique-2-bipartite modules. The list of biomarker genes discovered from these network modules are validated as the essential genes for causing a cancer in terms of network properties and survival analysis. This list of biomarker genes will help biologists to design wet lab experiments for further elucidating the complex mechanism of cancer.

scholarly journals Topological complexity of frictional interfaces: friction networks

2012 ◽  
Vol 19 (2) ◽  
pp. 215-225 ◽  
Author(s):  
H. O. Ghaffari ◽  
R. P. Young
Keyword(s):  
Topological Complexity ◽  
Type Ii ◽  
Stored Energy ◽  
Fracture Permeability ◽  
Radiated Energy ◽  
Universal Power Law ◽  
Shear Rupture ◽  
Crack Type ◽  
Network Properties ◽  
Highly Correlated

Abstract. Through research conducted in this study, a network approach to the correlation patterns of void spaces in rough fractures (crack type II) was developed. We characterized friction networks with several networks characteristics. The correlation among network properties with the fracture permeability is the result of friction networks. The revealed hubs in the complex aperture networks confirmed the importance of highly correlated groups to conduct the highlighted features of the dynamical aperture field. We found that there is a universal power law between the nodes' degree and motifs frequency (for triangles it reads T(k) ∝ kβ (β ≈ 2 ± 0.3)). The investigation of localization effects on eigenvectors shows a remarkable difference in parallel and perpendicular aperture patches. Furthermore, we estimate the rate of stored energy in asperities so that we found that the rate of radiated energy is higher in parallel friction networks than it is in transverse directions. The final part of our research highlights 4 point sub-graph distribution and its correlation with fluid flow. For shear rupture, we observed a similar trend in sub-graph distribution, resulting from parallel and transversal aperture profiles (a superfamily phenomenon).

scholarly journals Evidence and potential clinical significance of changes in gene network interactions in ovarian cancer

2015 ◽  
Vol 2 (1) ◽  
pp. 1
Author(s):  
Christopher G. Hill ◽  
John F. McDonald
Keyword(s):  
Ovarian Cancer ◽  
Epithelial Cells ◽  
Cancer Cells ◽  
Gene Network ◽  
Pearson Correlation ◽  
Regulatory Control ◽  
Ovarian Cancer Cells ◽  
New Class ◽  
Regulatory Mutations ◽  
Ovarian Surface Epithelial

The molecular basis of cancer is not merely the consequence of structural and/or regulatory mutations in genes, but additionally to disruptions in networks of regulatory interactions existing among these genes and other components of the genome. Disruptions in network relationships may manifest as the loss, gain or reversal of functionally significant interactive gene relationships in cancer cells. In this study, we first employ an unsupervised (Pearson correlation) approach to quantitatively estimate the overall change in network relationships between precursor (control) ovarian surface epithelial cells and ovarian cancer epithelial cells. We find that ovarian cancer cells display a significant overall reduction in correlated gene network interactions relative to normal precursor cells reflective of an overall loss of regulatory control.  We next focus on gene relationships that qualitatively change between normal and cancer samples. We find that biological processes significantly over represented among differentially expressed genes are substantially different from those associated with genes involved in qualitatively disrupted network interactions. Our findings provide novel insights into the processes underlying ovarian cancer and identify a potential new class of genes for targeted therapy.

scholarly journals Hematological and Genetic Predictors of Daytime Hemoglobin Saturation in Tanzanian Children with and without Sickle Cell Anemia

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Sharon E. Cox ◽  
Julie Makani ◽  
Charles R. Newton ◽  
Andrew M. Prentice ◽  
Fenella J. Kirkham
Keyword(s):  
Sickle Cell ◽  
Sickle Cell Anemia ◽  
Clinical Chemistry ◽  
Pearson Correlation ◽  
Transferrin Saturation ◽  
Full Blood Count ◽  
Hemoglobin F ◽  
Hemoglobin Saturation ◽  
Highly Correlated ◽  
Glucose 6 Phosphate Dehydrogenase

Low hemoglobin oxygen saturation (SpO2) is common in Sickle Cell Anemia (SCA) and associated with complications including stroke, although determinants remain unknown. We investigated potential hematological, genetic, and nutritional predictors of daytime SpO2 in Tanzanian children with SCA and compared them with non-SCA controls. Steady-state resting pulse oximetry, full blood count, transferrin saturation, and clinical chemistry were measured. Median daytime SpO2 was 97% (IQ range 94–99%) in SCA (N = 458), lower () than non-SCA (median 99%, IQ range 98–100%; N = 394). Within SCA, associations with SpO2 were observed for hematological variables, transferrin saturation, body-mass-index z-score, hemoglobin F (HbF%), genotypes, and hemolytic markers; mean cell hemoglobin (MCH) explained most variability (, Adj ). In non-SCA only age correlated with SpO2. -thalassemia 3.7 deletion highly correlated with decreased MCH (Pearson correlation coefficient 0.60, ). In multivariable models, lower SpO2 correlated with higher MCH (-coefficient 0.32, ) or with decreased copies of -thalassemia 3.7 deletion (-coefficient 1.1, ), and independently in both models with lower HbF% (-coefficient 0.15, ) and Glucose-6-Phosphate Dehydrogenase genotype (-coefficient 1.12, ). This study provides evidence to support the hypothesis that effects on red cell rheology are important in determining SpO2 in children with SCA. Potential mechanisms and implications are discussed.

scholarly journals Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Yang Bai ◽  
Laura Dougherty ◽  
Lailiang Cheng ◽  
Gan-Yuan Zhong ◽  
Kenong Xu
Keyword(s):  
Gene Network ◽  
Fruit Acidity ◽  
Network Modules

scholarly journals GOCI Yonsei Aerosol Retrieval (YAER) algorithm and validation during DRAGON-NE Asia 2012 campaign

2015 ◽  
Vol 8 (9) ◽  
pp. 9565-9609 ◽  
Author(s):  
M. Choi ◽  
J. Kim ◽  
J. Lee ◽  
M. Kim ◽  
Y. Je Park ◽  
...  
Keyword(s):  
Optical Properties ◽  
Land Surface ◽  
Pearson Correlation ◽  
Ocean Color ◽  
Single Scattering ◽  
Surface Reflectance ◽  
Robotic Networks ◽  
Deep Blue ◽  
Aerosol Retrieval ◽  
Highly Correlated

Abstract. The Geostationary Ocean Color Imager (GOCI) onboard the Communication, Ocean, and Meteorology Satellites (COMS) is the first multi-channel ocean color imager in geostationary orbit. Hourly GOCI top-of-atmosphere radiance has been available for the retrieval of aerosol optical properties over East Asia since March 2011. This study presents improvements to the GOCI Yonsei Aerosol Retrieval (YAER) algorithm over ocean and land together with validation results during the DRAGON-NE Asia 2012 campaign. Optical properties of aerosol are retrieved from the GOCI YAER algorithm including aerosol optical depth (AOD) at 550 nm, fine-mode fraction (FMF) at 550 nm, single scattering albedo (SSA) at 440 nm, Angstrom exponent (AE) between 440 and 860 nm, and aerosol type from selected aerosol models in calculating AOD. Assumed aerosol models are compiled from global Aerosol Robotic Networks (AERONET) inversion data, and categorized according to AOD, FMF, and SSA. Nonsphericity is considered, and unified aerosol models are used over land and ocean. Different assumptions for surface reflectance are applied over ocean and land. Surface reflectance over the ocean varies with geometry and wind speed, while surface reflectance over land is obtained from the 1–3 % darkest pixels in a 6 km × 6 km area during 30 days. In the East China Sea and Yellow Sea, significant area is covered persistently by turbid waters, for which the land algorithm is used for aerosol retrieval. To detect turbid water pixels, TOA reflectance difference at 660 nm is used. GOCI YAER products are validated using other aerosol products from AERONET and the MODIS Collection 6 aerosol data from "Dark Target (DT)" and "Deep Blue (DB)" algorithms during the DRAGON-NE Asia 2012 campaign from March to May 2012. Comparison of AOD from GOCI and AERONET gives a Pearson correlation coefficient of 0.885 and a linear regression equation with GOCI AOD =1.086 × AERONET AOD – 0.041. GOCI and MODIS AODs are more highly correlated over ocean than land. Over land, especially, GOCI AOD shows better agreement with MODIS DB than MODIS DT because of the choice of surface reflectance assumptions. Other GOCI YAER products show lower correlation with AERONET than AOD, but are still qualitatively useful.

scholarly journals Comparison of Fourier-Domain and Time-Domain Optical Coherence Tomography in the Measurement of Thinnest Corneal Thickness in Keratoconus

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Chunxiao Wang ◽  
Xueying Xia ◽  
Bishan Tian ◽  
Shiyou Zhou
Keyword(s):  
Optical Coherence Tomography ◽  
Time Domain ◽  
Pearson Correlation ◽  
Corneal Thickness ◽  
Intraclass Correlation ◽  
Fourier Domain ◽  
Optical Coherence ◽  
Highly Correlated ◽  
Time Domain Oct

Objective. To compare fourier-domain optical coherence tomography (FD-OCT) and time-domain OCT (TD-OCT) in the determination of thinnest corneal thickness (TCT).Methods. This study included 55 keratoconus patients and 50 healthy volunteers. The RTVue-OCT (FD-OCT) and Visante-OCT (TD-OCT) were used for the measurement of the TCT. Three consecutive scans were performed. The comparison and agreement between the two modalities were analyzed by pairedt-test, the Pearson correlation, intraclass correlation coefficient (ICC), and Bland-Altman plots. intraobserver repeatability was analyzed by the intraobserver within-subject standard deviation (S(w)), coefficient of variation (CV(w)), and ICC.Results. The TCT value of normal corneas was higher by RTVue-OCT (530.4 ± 19.7 μm) than Visante-OCT (521.5 ± 18.3 μm) (p<0.001). For keratoconus eyes, the TCT was 425.0 ± 58.2 μm and 424.4 ± 55.7 μm (difference being 0.6 ± 10.2 μm,p=0.604). Strong correlation (r= 0.938∼0.985) (ICC = 0.915–0.984) was observed between the two OCTs, and each OCT exhibited excellent repeatability in determining the TCT in all subjects (ICC = 0.984–0.994).Conclusions. The values of TCT obtained from RTVue-OCT and Visante-OCT were highly correlated; however, the two values were different. Both OCT instruments exhibited good intraobserver reliability. The existence of systematic differences suggested that the two instruments cannot be used interchangeably.

Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis

2019 ◽  
Vol 20 (1) ◽  
pp. 29-49 ◽  
Author(s):  
Shuchi Smita ◽  
Amit Katiyar ◽  
Sangram Keshari Lenka ◽  
Monika Dalal ◽  
Amish Kumar ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Network ◽  
Meta Analysis ◽  
Abiotic Stress Response ◽  
Network Modules ◽  
Rice Genotypes

scholarly journals National Airline Networks : A Graph Theoretic Analysis

2005 ◽  
Vol 19 (48) ◽  
pp. 461-474
Author(s):  
Siim Sööt
Keyword(s):  
Regression Analyses ◽  
Theoretic Analysis ◽  
Analytic Framework ◽  
Causal Factors ◽  
Network Characteristics ◽  
Graph Theoretic ◽  
Dependent Variables ◽  
Network Properties ◽  
Domestic Airline ◽  
Topographic Relief

Network properties of national domestic airline Systems are examined and linked to causal factors such as levels of economic development, population size and distribution, topographic relief, and size of country. Graph theoretic indices are utilized to measure network characteristics and become the independant variables in regression analyses. The theoretical pitfalls of this method are highlighted by utilizing a path analytic framework to identify the degree of interrelationship among the dependent variables. Still, the graph theoretic method is deemed useful as a means of topologic analysis of network structures.

Vital status ascertainment in cancerlinq discovery (CLQD): Improvement in mortality capture with a supplemental data source.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 7064-7064
Author(s):  
Danielle Potter ◽  
Melinda Kaltenbaugh ◽  
Shaum Kabadi ◽  
Aliki Taylor ◽  
Esther Pascual ◽  
...  
Keyword(s):  
Pearson Correlation ◽  
External Source ◽  
Real World Data ◽  
Clinical Cancer Research ◽  
Vital Status ◽  
Time To Death ◽  
External Data ◽  
Highly Correlated ◽  
Death Data

7064 Background: Overall survival (OS) is the gold standard outcome in clinical cancer research but many clinical trials cannot assess long-term OS. Real-world data sources can be used to calculate long-term OS, but only if vital status is accurately captured. Methods: The primary goal was to assess concordance of death dates from CLQD and an external source, and the effect of incorporation of external death data on estimates of OS. CLQD obtains electronic medical record (EMR) data from participating US oncology sites. Under-reporting of vital status is a common problem with EMR data; we investigated the value of including death data from a commercially available database, obituarydata.com (OBD) into CLQD. OBD pulls death data from published obituaries across the US. A matching algorithm is used to match patients in CLQD and OBD. OBD death data from breast, lung, ovarian, and pancreatic cancer patients diagnosed between 2010–2018 supplemented the CLQD in this study. OS was calculated using Kaplan-Meier estimation; Pearson correlation was used for comparing time to death. Results: The addition of OBD modestly changes OS estimates (see Table). Among a subset of patients with death dates in both CQLD and OBD, dates were highly correlated for breast (r = 0.98), lung (r = 0.93), ovarian (r = 0.99), and pancreatic (r = 0.88) cancers. When date differences existed, they were ≤10 days for > 95% of the patients. These results suggest death dates are reliable in CLQD EMRs. OS curves were as expected, with OS decreasing by stage and age at diagnosis. Conclusions: Incorporating OBD modestly improves OS estimates and shows that when death data is present in CLQD, it is reliable. Future enhancements will focus on improving sensitivity of mortality ascertainment with external data linkages, without compromising specificity. [Table: see text]

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