Semantics based approach for analyzing disease-target associations

Kaalia, Rama; Ghosh, Indira

doi:10.1016/j.jbi.2016.06.009

Cited by 4 publications

(3 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, cross talks in TGF-beta signalling is known to be involved in many developmental defects and cancer [ 36 ]. This observation concurs with homogeneity values derived in gene-disease associations (a type of functional interactions) in disease networks [ 24 , 37 ].…”

Section: Resultssupporting

confidence: 89%

Functional homogeneity and specificity of topological modules in human proteome

Kaalia

Rajapakse

2019

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

Background: Functional modules in protein-protein interaction networks (PPIN) are defined by maximal sets of functionally associated proteins and are vital to understanding cellular mechanisms and identifying disease associated proteins. Topological modules of the human proteome have been shown to be related to functional modules of PPIN. However, the effects of the weights of interactions between protein pairs and the integration of physical (direct) interactions with functional (indirect expression-based) interactions have not been investigated in the detection of functional modules of the human proteome. Results: We investigated functional homogeneity and specificity of topological modules of the human proteome and validated them with known biological and disease pathways. Specifically, we determined the effects on functional homogeneity and heterogeneity of topological modules (i) with both physical and functional protein-protein interactions; and (ii) with incorporation of functional similarities between proteins as weights of interactions. With functional enrichment analyses and a novel measure for functional specificity, we evaluated functional relevance and specificity of topological modules of the human proteome. Conclusions: The topological modules ranked using specificity scores show high enrichment with gene sets of known functions. Physical interactions in PPIN contribute to high specificity of the topological modules of the human proteome whereas functional interactions contribute to high homogeneity of the modules. Weighted networks result in more number of topological modules but did not affect their functional propensity. Modules of human proteome are more homogeneous for molecular functions than biological processes.

show abstract

Section: Resultssupporting

confidence: 89%

Functional homogeneity and specificity of topological modules in human proteome

Kaalia

Rajapakse

2019

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

show abstract

“…PageRank then computes the percent chance of arriving at any given webpage [10]. Notably, PageRank has been applied to many biological contexts including identifying candidate genes [11], topologically expressed genes [12], protein function prediction [13], gene evaluation from microarray results [14], finding functional gene modules [15, 16], entity linking [17], prioritizing transcriptional factors in gene regulatory networks [18], and semantic similarity for disease-target associations [19].…”

Section: Introductionmentioning

confidence: 99%

PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms

Solano,

D’Sa,

Nikolaidis

2024

Preprint

View full text Add to dashboard Cite

We herein report PageRankeR Gene Ontology (PRRGO), a downloadable web application that can integrate differentially expressed gene (DEG) data from the gene expression omnibus (GEO) GEO2R web tool with the gene ontology (GO) database. Unlike existing tools, PRRGO computes the PageRank for the entire GO network and can generate both interactive GO networks on the web interface and comma-separated values (CSV) files containing the DEG statistics categorized by GO term. These hierarchical and tabular GO-DEG data are especially conducive to hypothesis generation and overlap studies with the use of PageRank data, which can provide a metric of GO term centrality. We verified the tool for accuracy and reliability across nine independent heat shock (HS) studies for which the RNA-seq data was publicly available on GEO and found that the tool produced increasing concordance between study DEGs, GO terms, and select HS-specific GO terms.

show abstract

“…Researchers integrate disease ontology and symptom ontology by constructing the relationship between disease and symptoms [14]. Some progress has also been made in solving the problem of data resource linking [15].However, challenges remain, particularly in the realm of providing cues for misdiagnosis. Firstly, mainly anatomy-centric and lack semantic interconnections between concepts, thus failing to reflect similarities between symptoms.…”

Section: Introductionmentioning

confidence: 99%

Research on the Application of Semantic Network in Disease Diagnosis Prompts Based on Medical Corpus

Li,

Wang,

Yan

et al. 2024

IJIRCST

View full text Add to dashboard Cite

Portion of the causes of medical errors in outpatient clinics are incorrect treatment resulting from misdiagnosis. Misdiagnosis between diseases is often caused by similar and indistinguishable symptoms. Currently, disease knowledge and related symptom words that are prone to misdiagnosis are scattered in various medical literature or open online databases. Therefore, it is possible to merge symptom words of related diseases, build an ontology based on the semantic relationship between symptoms, and associate the association between diseases and symptoms. This project finally established the "Disease Symptoms" Semantic Network (DSSN). Using DSSN as a basic data set can serve as prompts for diseases that are easily misdiagnosed, assisting doctors in accurately diagnosing diseases. This plays a significant role in reducing the misdiagnosis rate.

show abstract

Semantics based approach for analyzing disease-target associations

Cited by 4 publications

References 67 publications

Functional homogeneity and specificity of topological modules in human proteome

Functional homogeneity and specificity of topological modules in human proteome

PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms

Research on the Application of Semantic Network in Disease Diagnosis Prompts Based on Medical Corpus

Contact Info

Product

Resources

About