the present paper aims at clarifying the role of the concept “walåyah” in the philosophy of the unity of being in islamic philosophy (waedat al-wujid). the concept “walåyah” is deeply built into the philosophic system of the islamic theory of being, and moreover the dynamic aspect of this concept has always activated islamic philosophy of existence and stimulated the thought of islamic philosop...

When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer ge...

Ontologies are being used nowadays in many areas, including bioinformatics. One of the issues in ontology research is the aligning and merging of ontologies. Tools have been developed for ontology merging, but they have not been evaluated for their use in bioinformatics. In this paper we evaluate two of the most well-known ontology merging tools with a bioinformatics perspective. As test ontolo...

An XML-based Java application is described that provides a function-oriented overview of the results of cluster analysis of gene-expression microarray data based on Gene Ontology terms and associations. The application generates one HTML page with listings of the frequencies of explicit and implicit Gene Ontology annotations for each cluster, and separate, linked pages with listings of explicit...

BACKGROUND Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. METHODS In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorp...

TP53 acts as a tumor suppressor in cancer. It induces cell cycle arrest or apoptosis in response to cellular stress and damage. p53 gene alteration could cause uncontrolled cell proliferation.In the present study, we used TP53 gene as the seed in the construction of a protein-protein functional association network to identify genes that might involve in tumorgenesis process with TP53. TP53 prot...

Background: Crohn's disease (CD) is a type of inflammatory bowel disease (IBD) which despite the unknown details is generally related to genetic, immune system, and environmental factors. In this study, we identify transcriptional signatures in patients with CD and then explain the potential molecular mechanisms in inflamed and non-inflamed intestinal mucosa in these patients. Materials and Me...

Abstract Q. liaotungensis is an important drought-resistant tree species in Northeast China where the climate dry and rainless. In this study, we performed a deep transcriptomic sequencing leaves, including de novo assembly functional annotation for screening candidate genes involved drought avoidance. A total of 25,593 unigenes were obtained from Illumina platform. According to Gene Ontology K...