Biological Pathway Extension Using Microarray Gene Expression Data

Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.

Study of Apoptosis and Gene Expression Pattern Related to Human Degenerative Intervertebral Disc Tissue / 中国康复理论与实践

@#ObjectiveTo investigate the relationship between the degenerative mechanisms of lumbar intervertebral disc (LID) and apoptosis.MethodsThe total RNAs were isolated from human LID tissues. Both the mRNAs from the degeneration and normal LID were reversely transcribed to the cDNAs. The cDNAs were labeled with the incorporations of fluorescent dUTP, for preparing the hybridization probes. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed by computer image analysis. The apoptotic status and the expression of Bcl-2 and Bax in 12 cases of degenerative LID and 10 cases of normal LID were detected with TdT-mediated dUTP-biotin nick end labeling (TUNEL) and immunohistochemistry methods.ResultsAmong the 4096 targets, there were 10 genes related to apoptosis. The expression related to Bax protein gene was up-regulated and it was down-regulated for Bcl-2 protein. In group of normal LID, the average apoptotic index (AI) was (24.897±3.620); percentage of Bcl-2 positive cells was (31.440±4.150)%; percentage of Bax positive cells was (29.372±2.588)%, average optical density (OD) values of positive particles were (0.183± 0.010 ), ( 0.203 ±0.012) and (0.169±0.005) respectively. In group of degenerative LID, the average AI was (49.232±3.440); percentage of Bcl-2 positive cells was (18.239±2.470)%; percentage of Bax positive cells was (52.349±3.764)%; average OD values of positive particles were (0.152±0.003), (0.310±0.008) and (0.262±0.014) respectively. There were significantly differences in AI and expressions of Bcl-2 and Bax proteins between normal LID and degenerative LID (P<0.05).ConclusionCell apoptosis plays an important role in the process of LID degeneration. Both Bcl-2 and Bax take part in the occurrence and progression of LID.

Analysis of Gene Expression Pattern of Lumbar Intervertebral Disc Degeneration in Human / 中国康复理论与实践

@#ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.