This study used DNA microarray data to identify differentially expressed genes of osteoporosis and provide useful information for treatments of the disease. We downloaded gene expression data of Osteoporosis GSE35956 from the Gene Expression Omnibus database, which included five normal and five osteoporosis samples. We then identified the differentially expressed genes between normal and diseas...

With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compati...

Demographic events such as migration, and evolutionary events like mutation and recombination, have contributed to the genetic variations that are found in the human genome. During the evolution and differentiation of human populations, different functional genes and pathways (a group of genes that act together to perform specific biological tasks) would have displayed different degrees of gene...

The number of complete and draft genomes has increased in recent years. The prediction of precise biological roles of the genes of such sequenced organisms is becoming an important issue in computational biology. We have recently developed two novel systems: KAAS (KEGG Automatic Annotation Server) [2, 4] and GENIES (Gene Network Inference Engine based on Supervised Analysis) [3] as computationa...

DINIES (drug-target interaction network inference engine based on supervised analysis) is a web server for predicting unknown drug-target interaction networks from various types of biological data (e.g. chemical structures, drug side effects, amino acid sequences and protein domains) in the framework of supervised network inference. The originality of DINIES lies in prediction with state-of-the...

Long noncoding RNA (lncRNA) plays roles in many diseases including asthma. Several lncRNAs function in the early differentiation of T-helper cells. lncRNA controls gene transcription, protein expression, and epigenetic regulation. Of the 4 asthma phenotypes, eosinophilic asthma (EA) is the most common. However, the lncRNAs associated with eosinophilic asthma have yet to be identified.We designe...

The objective of this study was the development of a gene/protein interaction network for primary myelofibrosis based on gene expression, and the enrichment analysis of KEGG pathways underlying the molecular complexes in this network. To achieve this, genes involved in primary myelofibrosis were selected from the OMIM database. A gene/protein interaction network for primary myelofibrosis was ob...

In this paper we survey work being conducted at Imperial College on the use of machine learning to build Systems Biology models of the effects of toxins on biochemical pathways. Several distinct, and complementary modelling techniques are being explored. Firstly, work is being conducted on applying Support-Vector ILP (SVILP) as an accurate means of screening high-toxicity molecules. Secondly, B...

It is well known spinal cord injury (SCI) can cause chronic neuropathic pain (NP); however its underlying molecular mechanisms remain elusive. This study aimed to disclose differentially expressed genes (DEGs) and activated signaling pathways in association with SCI induced chronic NP, in order to identify its diagnostic and therapeutic targets. Microarray dataset GSE5296 has been downloaded fr...

This package implements the Signaling Pathway Impact Analysis (SPIA) algorithm described in Tarca et al. (2009), Khatri et al. (2007) and Draghici et al. (2007). SPIA uses the information from a set of differentially expressed genes and their fold changes, as well as pathways topology in order to assess the significance of the pathways in the condition under the study. The current version of SP...