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Network-based gene expression biomarkers for cold and heat patterns of rheumatoid arthritis in traditional chinese medicine.

Lu C, Niu X, Xiao C, Chen G, Zha Q, Guo H, Jiang M, Lu A - Evid Based Complement Alternat Med (2012)

Bottom Line: IN TRADITIONAL CHINESE MEDICINE (TCM), PATIENTS WITH RHEUMATOID ARTHRITIS (RA) CAN BE CLASSIFIED INTO TWO MAIN PATTERNS: cold-pattern and heat-pattern.Gene expression profilings of CD4+ T cells from cold-pattern RA patients, heat-pattern RA patients, and healthy volunteers were obtained using microarray.PRKAA1, HSPA8, and LSM6, which were related to fatty acid metabolism and the I-κB kinase/NF-κB cascade, were significant biomarkers of the TCM heat-pattern of RA.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Science, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China.

ABSTRACT
IN TRADITIONAL CHINESE MEDICINE (TCM), PATIENTS WITH RHEUMATOID ARTHRITIS (RA) CAN BE CLASSIFIED INTO TWO MAIN PATTERNS: cold-pattern and heat-pattern. This paper identified the network-based gene expression biomarkers for both cold- and heat-patterns of RA. Gene expression profilings of CD4+ T cells from cold-pattern RA patients, heat-pattern RA patients, and healthy volunteers were obtained using microarray. The differentially expressed genes and related networks were explored using DAVID, GeneSpring software, and the protein-protein interactions (PPI) method. EIF4A2, CCNT1, and IL7R, which were related to the up-regulation of cell proliferation and the Jak-STAT cascade, were significant gene biomarkers of the TCM cold pattern of RA. PRKAA1, HSPA8, and LSM6, which were related to fatty acid metabolism and the I-κB kinase/NF-κB cascade, were significant biomarkers of the TCM heat-pattern of RA. The network-based gene expression biomarkers for the TCM cold- and heat-patterns may be helpful for the further stratification of RA patients when deciding on interventions or clinical trials.

No MeSH data available.


Related in: MedlinePlus

The PPI subnetworks based on the differently expressed genes made up of highly connected regions. (a–d): The subnetworks of the cold pattern versus control comparison. (e–h): The subnetworks of the heat pattern versus control comparison. Diamonds represent seed nodes. Cycles represent neighbor nodes. All edges represent interactions.
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fig3: The PPI subnetworks based on the differently expressed genes made up of highly connected regions. (a–d): The subnetworks of the cold pattern versus control comparison. (e–h): The subnetworks of the heat pattern versus control comparison. Diamonds represent seed nodes. Cycles represent neighbor nodes. All edges represent interactions.

Mentions: The PPI networks of the significantly expressed genes between the cold pattern and the control and between the heat pattern and the control are shown in Figure 3. There were four subnetworks for the cold-pattern comparison and four subnetworks for the heat patten comparison. The gene ontology analyses of each subnetwork are shown in Table 10.


Network-based gene expression biomarkers for cold and heat patterns of rheumatoid arthritis in traditional chinese medicine.

Lu C, Niu X, Xiao C, Chen G, Zha Q, Guo H, Jiang M, Lu A - Evid Based Complement Alternat Med (2012)

The PPI subnetworks based on the differently expressed genes made up of highly connected regions. (a–d): The subnetworks of the cold pattern versus control comparison. (e–h): The subnetworks of the heat pattern versus control comparison. Diamonds represent seed nodes. Cycles represent neighbor nodes. All edges represent interactions.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3318903&req=5

fig3: The PPI subnetworks based on the differently expressed genes made up of highly connected regions. (a–d): The subnetworks of the cold pattern versus control comparison. (e–h): The subnetworks of the heat pattern versus control comparison. Diamonds represent seed nodes. Cycles represent neighbor nodes. All edges represent interactions.
Mentions: The PPI networks of the significantly expressed genes between the cold pattern and the control and between the heat pattern and the control are shown in Figure 3. There were four subnetworks for the cold-pattern comparison and four subnetworks for the heat patten comparison. The gene ontology analyses of each subnetwork are shown in Table 10.

Bottom Line: IN TRADITIONAL CHINESE MEDICINE (TCM), PATIENTS WITH RHEUMATOID ARTHRITIS (RA) CAN BE CLASSIFIED INTO TWO MAIN PATTERNS: cold-pattern and heat-pattern.Gene expression profilings of CD4+ T cells from cold-pattern RA patients, heat-pattern RA patients, and healthy volunteers were obtained using microarray.PRKAA1, HSPA8, and LSM6, which were related to fatty acid metabolism and the I-κB kinase/NF-κB cascade, were significant biomarkers of the TCM heat-pattern of RA.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Science, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China.

ABSTRACT
IN TRADITIONAL CHINESE MEDICINE (TCM), PATIENTS WITH RHEUMATOID ARTHRITIS (RA) CAN BE CLASSIFIED INTO TWO MAIN PATTERNS: cold-pattern and heat-pattern. This paper identified the network-based gene expression biomarkers for both cold- and heat-patterns of RA. Gene expression profilings of CD4+ T cells from cold-pattern RA patients, heat-pattern RA patients, and healthy volunteers were obtained using microarray. The differentially expressed genes and related networks were explored using DAVID, GeneSpring software, and the protein-protein interactions (PPI) method. EIF4A2, CCNT1, and IL7R, which were related to the up-regulation of cell proliferation and the Jak-STAT cascade, were significant gene biomarkers of the TCM cold pattern of RA. PRKAA1, HSPA8, and LSM6, which were related to fatty acid metabolism and the I-κB kinase/NF-κB cascade, were significant biomarkers of the TCM heat-pattern of RA. The network-based gene expression biomarkers for the TCM cold- and heat-patterns may be helpful for the further stratification of RA patients when deciding on interventions or clinical trials.

No MeSH data available.


Related in: MedlinePlus