Limits...
Prediction and Characterisation of the System Effects of Aristolochic Acid: A Novel Joint Network Analysis towards Therapeutic and Toxicological Mechanisms.

Nie W, Lv Y, Yan L, Chen X, Lv H - Sci Rep (2015)

Bottom Line: However, the molecular mechanisms of AA systems effects remain poorly understood.Here, we employed a joint network analysis that combines network pharmacology, a protein-protein interaction (PPI) database, biological processes analysis and functional annotation analysis to explore system effects.Thirdly, the pathway-based functional enrichment analysis was manipulated using WebGestalt to identify the mostly significant pathways associated with AA.

View Article: PubMed Central - PubMed

Affiliation: Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing 401331, P.R. China.

ABSTRACT
Aristolochic acid (AA) is the major active component of medicinal plants from the Aristolochiaceae family of flowering plants widely utilized for medicinal purposes. However, the molecular mechanisms of AA systems effects remain poorly understood. Here, we employed a joint network analysis that combines network pharmacology, a protein-protein interaction (PPI) database, biological processes analysis and functional annotation analysis to explore system effects. Firstly, we selected 15 protein targets (14 genes) in the PubChem database as the potential target genes and used PPI knowledge to incorporate these genes into an AA-specific gene network that contains 129 genes. Secondly, we performed biological processes analysis for these AA-related targets using ClueGO, some of new targeted genes were randomly selected and experimentally verified by employing the Quantitative Real-Time PCR assay for targeting the systems effects of AA in HK-2 cells with observed dependency of concentration. Thirdly, the pathway-based functional enrichment analysis was manipulated using WebGestalt to identify the mostly significant pathways associated with AA. At last, we built an AA target pathway network of significant pathways to predict the system effects. Taken together, this joint network analysis revealed that the systematic regulatory effects of AA on multidimensional pathways involving both therapeutic action and toxicity.

No MeSH data available.


Related in: MedlinePlus

Network groupings based on functionally enriched BP terms.(A) A functionally grouped network of enriched categories was generated for AA-related targets using GO terms as nodes and linked using ClueGO analysis. Only the most significant terms in the group are labelled. Functionally related groups partially overlap. (B) Functional groups and their corresponding colours.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664954&req=5

f5: Network groupings based on functionally enriched BP terms.(A) A functionally grouped network of enriched categories was generated for AA-related targets using GO terms as nodes and linked using ClueGO analysis. Only the most significant terms in the group are labelled. Functionally related groups partially overlap. (B) Functional groups and their corresponding colours.

Mentions: To annotate the biological functions of AA-related targets, we manipulated the functional enrichment analyses using Gene Ontology (GO) terms and further evaluated the biological processes (BPs) term using the Cytoscape plug-in ClueGO. Overall, 178 GO terms were significantly enriched, as shown in Fig. 5A. These GO terms have been categorised into 21 sub-groups, as shown in Fig. 5B, which primarily involve in liver development, positive regulation of apoptotic process, and cell-type specific apoptotic process.


Prediction and Characterisation of the System Effects of Aristolochic Acid: A Novel Joint Network Analysis towards Therapeutic and Toxicological Mechanisms.

Nie W, Lv Y, Yan L, Chen X, Lv H - Sci Rep (2015)

Network groupings based on functionally enriched BP terms.(A) A functionally grouped network of enriched categories was generated for AA-related targets using GO terms as nodes and linked using ClueGO analysis. Only the most significant terms in the group are labelled. Functionally related groups partially overlap. (B) Functional groups and their corresponding colours.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664954&req=5

f5: Network groupings based on functionally enriched BP terms.(A) A functionally grouped network of enriched categories was generated for AA-related targets using GO terms as nodes and linked using ClueGO analysis. Only the most significant terms in the group are labelled. Functionally related groups partially overlap. (B) Functional groups and their corresponding colours.
Mentions: To annotate the biological functions of AA-related targets, we manipulated the functional enrichment analyses using Gene Ontology (GO) terms and further evaluated the biological processes (BPs) term using the Cytoscape plug-in ClueGO. Overall, 178 GO terms were significantly enriched, as shown in Fig. 5A. These GO terms have been categorised into 21 sub-groups, as shown in Fig. 5B, which primarily involve in liver development, positive regulation of apoptotic process, and cell-type specific apoptotic process.

Bottom Line: However, the molecular mechanisms of AA systems effects remain poorly understood.Here, we employed a joint network analysis that combines network pharmacology, a protein-protein interaction (PPI) database, biological processes analysis and functional annotation analysis to explore system effects.Thirdly, the pathway-based functional enrichment analysis was manipulated using WebGestalt to identify the mostly significant pathways associated with AA.

View Article: PubMed Central - PubMed

Affiliation: Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing 401331, P.R. China.

ABSTRACT
Aristolochic acid (AA) is the major active component of medicinal plants from the Aristolochiaceae family of flowering plants widely utilized for medicinal purposes. However, the molecular mechanisms of AA systems effects remain poorly understood. Here, we employed a joint network analysis that combines network pharmacology, a protein-protein interaction (PPI) database, biological processes analysis and functional annotation analysis to explore system effects. Firstly, we selected 15 protein targets (14 genes) in the PubChem database as the potential target genes and used PPI knowledge to incorporate these genes into an AA-specific gene network that contains 129 genes. Secondly, we performed biological processes analysis for these AA-related targets using ClueGO, some of new targeted genes were randomly selected and experimentally verified by employing the Quantitative Real-Time PCR assay for targeting the systems effects of AA in HK-2 cells with observed dependency of concentration. Thirdly, the pathway-based functional enrichment analysis was manipulated using WebGestalt to identify the mostly significant pathways associated with AA. At last, we built an AA target pathway network of significant pathways to predict the system effects. Taken together, this joint network analysis revealed that the systematic regulatory effects of AA on multidimensional pathways involving both therapeutic action and toxicity.

No MeSH data available.


Related in: MedlinePlus