scholarly journals MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Luman Wang ◽  
Qiaochu Mo ◽  
Jianxin Wang
Keyword(s):  
Mutual Information ◽  
Immune Cells ◽  
Linear Correlation ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Specific Gene ◽  
Nonlinear Correlation ◽  
Gene Coexpression ◽  
Human Genes ◽  
Cell Groups

Most current gene coexpression databases support the analysis for linear correlation of gene pairs, but not nonlinear correlation of them, which hinders precisely evaluating the gene-gene coexpression strengths. Here, we report a new database, MIrExpress, which takes advantage of the information theory, as well as the Pearson linear correlation method, to measure the linear correlation, nonlinear correlation, and their hybrid of cell-specific gene coexpressions in immune cells. For a given gene pair or probe set pair input by web users, both mutual information (MI) and Pearson correlation coefficient (r) are calculated, and several corresponding values are reported to reflect their coexpression correlation nature, including MI andrvalues, their respective rank orderings, their rank comparison, and their hybrid correlation value. Furthermore, for a given gene, the top 10 most relevant genes to it are displayed with the MI,r, or their hybrid perspective, respectively. Currently, the database totally includes 16 human cell groups, involving 20,283 human genes. The expression data and the calculated correlation results from the database are interactively accessible on the web page and can be implemented for other related applications and researches.

scholarly journals Operational Risk Aggregation Based on Business Line Dependence: A Mutual Information Approach

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Wenzhou Wang ◽  
Limeng Shi ◽  
Xiaoqian Zhu
Keyword(s):  
Mutual Information ◽  
Correlation Coefficient ◽  
Linear Correlation ◽  
Risk Estimation ◽  
Pearson Correlation ◽  
Operational Risk ◽  
Random Variable ◽  
Data Set ◽  
Risk Aggregation ◽  
Business Line

The dependencies between different business lines of banks have serious effects on the accuracy of operational risk estimation. Furthermore, the dependencies are far more complicated than simple linear correlation. While Pearson correlation coefficient is constructed based on the hypothesis of a linear association, the mutual information that measures all the information of a random variable contained in another random variable is a powerful alternative. Based on mutual information, the generalized correlation coefficient which can capture both linear and nonlinear correlation can be derived. This paper models the correlation between business lines by mutual information and normal copula. The experiment on a real-world Chinese bank operational risk data set shows that using mutual information to model the dependencies between business lines is more reasonable than linear correlation.

scholarly journals Robust gene coexpression networks using signed distance correlation

2021 ◽  
Author(s):  
Javier Pardo-Diaz ◽  
Lyuba V Bozhilova ◽  
Mariano Beguerisse-Díaz ◽  
Philip S Poole ◽  
Charlotte M Deane ◽  
...  
Keyword(s):  
Mutual Information ◽  
Pearson Correlation ◽  
Biological Information ◽  
Supplementary Information ◽  
Functional Information ◽  
Distance Correlation ◽  
Functional Annotations ◽  
Signed Distance ◽  
Gene Coexpression ◽  
Coexpression Networks

Abstract Motivation Even within well studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information. Results We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods such as Pearson correlation and mutual information. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson correlation or mutual information. Supplementary information Supplementary Information and code are available at Bioinformatics and https://github.com/javier-pardodiaz/sdcorGCN online.

scholarly journals The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chuxiang Lei ◽  
Dan Yang ◽  
Wenlin Chen ◽  
Haoxuan Kan ◽  
Fang Xu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Clinical Significance ◽  
Immune Cells ◽  
Complement System ◽  
Aortic Wall ◽  
Gene Coexpression Network ◽  
Hub Genes ◽  
Gene Coexpression ◽  
The Complement System ◽  
Coexpression Network Analysis

Abstract Background Thoracic aortic aneurysm (TAA) can be life-threatening due to the progressive weakening and dilatation of the aortic wall. Once the aortic wall has ruptured, no effective pharmaceutical therapies are available. However, studies on TAA at the gene expression level are limited. Our study aimed to identify the driver genes and critical pathways of TAA through gene coexpression networks. Methods We analyzed the genetic data of TAA patients from a public database by weighted gene coexpression network analysis (WGCNA). Modules with clinical significance were identified, and the differentially expressed genes (DEGs) were intersected with the genes in these modules. Gene Ontology and pathway enrichment analyses were performed. Finally, hub genes that might be driving factors of TAA were identified. Furthermore, we evaluated the diagnostic accuracy of these genes and analyzed the composition of immune cells using the CIBERSORT algorithm. Results We identified 256 DEGs and two modules with clinical significance. The immune response, including leukocyte adhesion, mononuclear cell proliferation and T cell activation, was identified by functional enrichment analysis. CX3CR1, C3, and C3AR1 were the top 3 hub genes in the module correlated with TAA, and the areas under the curve (AUCs) by receiver operating characteristic (ROC) analysis of all the hub genes exceeded 0.7. Finally, we found that the proportions of infiltrating immune cells in TAA and normal tissues were different, especially in terms of macrophages and natural killer (NK) cells. Conclusion Chemotaxis and the complement system were identified as crucial pathways in TAA, and macrophages with interactive immune cells may regulate this pathological process.

Should CD138 Immunohistochemistry be Standard Recommended Practice for Bone Marrow Evaluation of Plasma Cell Neoplasms?

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S110-S110
Author(s):  
A Vijayanarayanan ◽  
K Inamdar ◽  
M Menon ◽  
P Kuriakose
Keyword(s):  
Bone Marrow ◽  
Plasma Cell ◽  
Linear Correlation ◽  
Plasma Cells ◽  
Pearson Correlation ◽  
Protein Electrophoresis ◽  
Pearson Correlation Coefficient ◽  
Cell Percentage ◽  
Significant Linear Correlation ◽  
Plasma Cell Neoplasms

Abstract Introduction/Objective Myeloma diagnosis by a pathologist requires 10% plasma cells (PC) or a biopsy proven plasmacytoma in addition to myeloma defining events. PC% > 60% is a biomarker of malignancy under this definition. WHO allows for assesment of plasma cell percentage either by aspirate count or by CD138 immunohistochemistry (IHC). There is lack of consensus on aspirate smear adequacy for PC% estimation. Uneven distribution of plasma cells, hemodilution and/or patchy infiltration can lead to gross underestimation. We compared PC% by aspirate count and CD138 IHC and established corelation with serum protein electrophoresis (SPEP) values. Methods 67 myeloma cases were included after excluding cases with suboptimal or inadequate aspirate smears. Two hematopathologists evaluated the diagnostic marrow (therapy naive) for PC% by aspirate count and CD138 IHC on biopsy/clot section. Corresponding SPEP and Free light chain (FLC) values were obtained. Correlation coefficent was calculated using Pearson correlation coefficient (GraphPad Prism). Results The Ig subtypes included IgG (41/67) and IgA (17/67). 12 cases had available FLC values. Both average and median PC% by CD138 IHC was considerably higher (50%, 52%) compared to aspirate count (29%, 21%). However, PC% by aspirate smear count and CD138 IHC demonstrated a significant linear correlation (r=0.71, p60% by CD138 (and not by aspirate count). Conclusion CD138 IHC based PC% is consistently higher, nevertheless, statistically significant linear corelation is observed between aspirate count PC% and CD138 IHC. A significant linear correlation is observed between CD138 IHC and SPEP (IgG and IgA), however, no such correlation is observed with aspirate count. More cases were diagnosed as myeloma (11%) and higher propotion of cases (35%) had biomarker of malignancy i.e. PC% >60% by CD138 IHC. Based on these findings, we propose estimation of PC% by CD138 immunostain be a recommended standard practice for better clinicopathologic and biologic correlation.

Screening of Biosurfactant Producing Bacteria Isolated from Hydrocarbon Contaminated Site and Their Potential in Biosorption of Pb(II) and Oil Biodegradation

2021 ◽  
Vol 58 (6) ◽  
pp. 435-441
Author(s):  
Swati Rastogi ◽  
Sheel Ratna ◽  
Rajesh Kumar
Keyword(s):  
High Efficiency ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Contaminated Site ◽  
Screening Methods ◽  
Motor Oil ◽  
Bacterial Strains ◽  
Biosorption Process ◽  
Used Motor Oil ◽  
Haemolytic Assay

Abstract In the present study, three potentially Pb(II)-resistant and biosurfactant-producing bacterial strains were isolated from a total of 23 strains using various screening methods, investigated for their biosorption of Pb(II) and used for the biodegradation of used motor oil. The results show that strain E1 (Bacillus haynesii) has significantly high efficiency in biodegradation of used motor oil, up to 82 % in the first three days. Maximum Pb(II) biosorption capacities of 238.09 mg/g and 99.01 mg/g were determined for strains E1 and F5 (Pseudomonas aeruginosa), respectively. The biosorption process was found to be in good agreement with the Langmuir isotherm for both E1 (R2 = 0.9614) and F5 (R2 = 0.9646), suggesting monolayer biosorption. The four common screening methods, namely the haemolytic assay, the determination of surface tension, the emulsifying activity and the foam test, were also correlated with the Pearson correlation method.

scholarly journals Loss of critical developmental and human disease-causing genes in 58 mammals

2019 ◽  
Author(s):  
Yatish Turakhia ◽  
Heidi I. Chen ◽  
Amir Marcovitz ◽  
Gill Bejerano
Keyword(s):  
Evolutionary Biology ◽  
Large Scale ◽  
Gene Annotation ◽  
Synonymous Substitution ◽  
Specific Gene ◽  
High Confidence ◽  
Protein Coding ◽  
Congenital Diseases ◽  
Manual Curation ◽  
Human Genes

Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools and protein databases focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (deletion and non-synonymous substitution) as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence protein-coding gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using the hg38 human assembly as a reference, we discovered over 500 unique human genes affected by such high-confidence erosion events in different clades across 58 mammals. While most of these events likely have benign consequences, we also found dozens of clade-specific gene losses that result in early lethality in outgroup mammals or are associated with severe congenital diseases in humans. Our discoveries yield intriguing potential for translational medical genetics and for evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.

scholarly journals Features of the cytokine balance in infectious hemorrhagic colitis in children

2019 ◽  
Vol 18 (3) ◽  
pp. 11-16 ◽  
Author(s):  
O. I. Klimova ◽  
N. V. Gonchar ◽  
Yu. V. Lobzin ◽  
L. A. Alekseeva ◽  
N. E. Monakhova
Keyword(s):  
Young Children ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Relative Number ◽  
Suppressive Effect ◽  
Hemorrhagic Colitis ◽  
Cytokine Balance ◽  
Severity Of The Disease ◽  
Relationship Of ◽  
The Relationship

The aim of the study was to study the features of cytokine balance and their effect on clinical and laboratory parameters in infectious hemorrhagic colitis in children. Materials and methods. In the Department of intestinal infections in 2018 observed 28 children with infectious haemorrhagic colitis. The diagnosis was established taking into account clinical recommendations; the severity of the disease was determined by the Clark index; the etiology was verified according to bacteriological and molecular studies of feces, serological methods. In the acute period of the disease, the concentration of cytokines in the blood serum — TNF-a, IL-4, IL-6, IL-10 was studied by enzyme immunoassay. Mann-Whitney method, Kruskal-Wallis dispersion analysis, Pearson correlation method we used to estimate the obtained data.Results. The age structure of patients was dominated by young children (53.6%). Mild form of the disease was diagnosed in 32.1% of patients, moderate — in 67.9%. A high level of IL-4 was observed against a relatively low level of TNF-a, IL-6 and IL-10. Significantly higher concentrations of TNF-a and IL-6 were found in children with moderate form of the disease. The maximum values of IL-6 were observed in young children, IL-10 — in infants. In the moderate form of the disease, negative correlations of IL-4 with the number of leukocytes (r = –0.46; p = 0.05) and platelets (r = –0.48; p < 0.05) in the hemogram noted. Early age patients were found to have correlations of TNF-a with the relative number of rod neutrophils (r = 0.62; p < 0.01). There was a significant correlation of IL-4 with the relative number of segmental neutrophils (r = 0.49; p < 0.05). The relationship of TNF-a with the severity of the disease (r = 0.42; p < 0.05) revealed. The data on the possible suppressive effect of TNF-a and IL-10 on the synthesis of urea and the relationship of IL-6 with reactive changes in the liver obtained.Conclusion. Studies of cytokine balance in infectious hemorrhagic colitis in children showed the severity of systemic inflammatory response with the activation of Th-2 immune response. The correlation of TNF-a with the severity of the disease was established, which may have diagnostic and prognostic value.

scholarly journals Do aggression and impulsivity dominate dark triad across genders?

2020 ◽  
Author(s):  
Anupriya Singh ◽  
Aisha Naeem ◽  
Komal Chandiramani
Keyword(s):  
Gender Differences ◽  
Standard Deviation ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Dark Triad ◽  
T Test ◽  
Descriptive Statistics ◽  
Regression Analyses ◽  
Future Directions ◽  
Significant Relationships

The study investigated gender differences in Overall Dark Triad (Machiavellianism, Narcissism, and Psychopathy), Aggression, Impulsivity, and impact of Dark triad on Aggression and Impulsivity. Data was collected from 214 young adults. Analyses was done using descriptive statistics (mean and standard deviation). T-test was employed to analyze gender differences. Pearson Correlation Method and Multiple regression were used to assess the relation and prediction amongst the variables, respectively. T-test suggested significant gender differences in Machiavellianism, Psychopathy, and Overall Dark Triad, with females scoring high than males. No gender difference was observed in Aggression and Impulsivity. Correlation and regression analyses revealed several significant relationships between the above constructs. The research was concluded by briefly foregrounding some of the study’s implications and future directions.

scholarly journals PENGUKURAN TRANSPARANSI KEUANGAN DAERAH BERBASIS WEBSITE PADA KABUPATEN/KOTA DI INDONESIA

2019 ◽  
Vol 4 (1) ◽  
pp. 153
Author(s):  
Muhammad Rizki Alwahidi ◽  
Darwanis Darwanis
Keyword(s):  
Local Government ◽  
Pearson Correlation ◽  
Correlation Method ◽  
Average Level ◽  
Probability Sampling ◽  
Financial Transparency

The purpose of this study was to measure the level of regional financial transparency and see the correlations between the wealth of the local government and BPK's opinion on the level of regional financial transparency in districts / cities in Indonesia. The sample taken in this study is probability sampling with Slovin method. The number of samples used in this study is 224 districts / cities. The data obtained were analyzed using Simple Pearson correlation method. The results of this study indicate that the average level of regional financial transparency in districts / cities in Indonesia is 18.85%. The highest value is 71% obtained by Natuna Regency and the lowest value is 2.09 obtained by 48 regencies / cities in Indonesia. The results of this study also show that the level of local government wealth and BPK's Opinion have a very low relationship to the level of regional financial transparency.

scholarly journals Visualization of Correlation for Air Pollution Time Series using TAQMN Data

2019 ◽  
Vol 8 (3) ◽  
pp. 7922-7927
Keyword(s):  
Air Pollution ◽  
Time Series ◽  
Particulate Matter ◽  
Pearson Correlation ◽  
Fine Particulate Matter ◽  
Correlation Method ◽  
Well Being ◽  
Pollution Levels ◽  
Fine Particulate ◽  
Pm2.5 Concentration

In Taiwan country Annan, Chiayi, Giran, and Puzi cities are facing a serious fine particulate matter (PM2.5) issue. To date the impressive advance has been made toward understanding the PM2.5 issue, counting special temporal characterization, driving variables and well-being impacted. However, notable research as has been done on the interaction of the content between the selected cities of Taiwan country for particulate matter (PM2.5) concentration. In this paper, we purposed a visualization technique based on this principle of the visualization, cross-correlation method and also the time-series concentration with particulate matter (PM2.5) for different cities in Taiwan. The visualization also shows that the correlation between the different meteorological factors as well as the different air pollution pollutants for particular cities in Taiwan. This visualization approach helps to determine the concentration of the air pollution levels in different cities and also determine the Pearson correlation, r values of selected cities are Annan, Puzi, Giran, and Wugu.

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