Tags

Type your tag names separated by a space and hit enter

Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae.
BMC Bioinformatics 2010; 11 Suppl 11:S6BB

Abstract

BACKGROUND

Traditional Chinese Medicine (TCM) is characterized by the wide use of herbal formulae, which are capable of systematically treating diseases determined by interactions among various herbs. However, the combination rule of TCM herbal formulae remains a mystery due to the lack of appropriate methods.

METHODS

From a network perspective, we established a method called Distance-based Mutual Information Model (DMIM) to identify useful relationships among herbs in numerous herbal formulae. DMIM combines mutual information entropy and "between-herb-distance" to score herb interactions and construct herb network. To evaluate the efficacy of the DMIM-extracted herb network, we conducted in vitro assays to measure the activities of strongly connected herbs and herb pairs. Moreover, using the networked Liu-wei-di-huang (LWDH) formula as an example, we proposed a novel concept of "co-module" across herb-biomolecule-disease multilayer networks to explore the potential combination mechanism of herbal formulae.

RESULTS

DMIM, when used for retrieving herb pairs, achieves a good balance among the herb's frequency, independence, and distance in herbal formulae. A herb network constructed by DMIM from 3865 Collaterals-related herbal formulae can not only nicely recover traditionally-defined herb pairs and formulae, but also generate novel anti-angiogenic herb ingredients (e.g. Vitexicarpin with IC50=3.2 μM, and Timosaponin A-III with IC50=3.4 μM) as well as herb pairs with synergistic or antagonistic effects. Based on gene and phenotype information associated with both LWDH herbs and LWDH-treated diseases, we found that LWDH-treated diseases show high phenotype similarity and identified certain "co-modules" enriched in cancer pathways and neuro-endocrine-immune pathways, which may be responsible for the action of treating different diseases by the same LWDH formula.

CONCLUSIONS

DMIM is a powerful method to identify the combination rule of herbal formulae and lead to new discoveries. We also provide the first evidence that the co-module across multilayer networks may underlie the combination mechanism of herbal formulae and demonstrate the potential of network biology approaches in the studies of TCM.

Authors+Show Affiliations

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing, China. shaoli@mail.tsinghua.edu.cnNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21172056

Citation

Li, Shao, et al. "Herb Network Construction and Co-module Analysis for Uncovering the Combination Rule of Traditional Chinese Herbal Formulae." BMC Bioinformatics, vol. 11 Suppl 11, 2010, pp. S6.
Li S, Zhang B, Jiang D, et al. Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics. 2010;11 Suppl 11:S6.
Li, S., Zhang, B., Jiang, D., Wei, Y., & Zhang, N. (2010). Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics, 11 Suppl 11, pp. S6. doi:10.1186/1471-2105-11-S11-S6.
Li S, et al. Herb Network Construction and Co-module Analysis for Uncovering the Combination Rule of Traditional Chinese Herbal Formulae. BMC Bioinformatics. 2010 Dec 14;11 Suppl 11:S6. PubMed PMID: 21172056.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. AU - Li,Shao, AU - Zhang,Bo, AU - Jiang,Duo, AU - Wei,Yingying, AU - Zhang,Ningbo, Y1 - 2010/12/14/ PY - 2010/12/22/entrez PY - 2011/1/5/pubmed PY - 2011/6/9/medline SP - S6 EP - S6 JF - BMC bioinformatics JO - BMC Bioinformatics VL - 11 Suppl 11 N2 - BACKGROUND: Traditional Chinese Medicine (TCM) is characterized by the wide use of herbal formulae, which are capable of systematically treating diseases determined by interactions among various herbs. However, the combination rule of TCM herbal formulae remains a mystery due to the lack of appropriate methods. METHODS: From a network perspective, we established a method called Distance-based Mutual Information Model (DMIM) to identify useful relationships among herbs in numerous herbal formulae. DMIM combines mutual information entropy and "between-herb-distance" to score herb interactions and construct herb network. To evaluate the efficacy of the DMIM-extracted herb network, we conducted in vitro assays to measure the activities of strongly connected herbs and herb pairs. Moreover, using the networked Liu-wei-di-huang (LWDH) formula as an example, we proposed a novel concept of "co-module" across herb-biomolecule-disease multilayer networks to explore the potential combination mechanism of herbal formulae. RESULTS: DMIM, when used for retrieving herb pairs, achieves a good balance among the herb's frequency, independence, and distance in herbal formulae. A herb network constructed by DMIM from 3865 Collaterals-related herbal formulae can not only nicely recover traditionally-defined herb pairs and formulae, but also generate novel anti-angiogenic herb ingredients (e.g. Vitexicarpin with IC50=3.2 μM, and Timosaponin A-III with IC50=3.4 μM) as well as herb pairs with synergistic or antagonistic effects. Based on gene and phenotype information associated with both LWDH herbs and LWDH-treated diseases, we found that LWDH-treated diseases show high phenotype similarity and identified certain "co-modules" enriched in cancer pathways and neuro-endocrine-immune pathways, which may be responsible for the action of treating different diseases by the same LWDH formula. CONCLUSIONS: DMIM is a powerful method to identify the combination rule of herbal formulae and lead to new discoveries. We also provide the first evidence that the co-module across multilayer networks may underlie the combination mechanism of herbal formulae and demonstrate the potential of network biology approaches in the studies of TCM. SN - 1471-2105 UR - https://www.unboundmedicine.com/medline/citation/21172056/Herb_network_construction_and_co_module_analysis_for_uncovering_the_combination_rule_of_traditional_Chinese_herbal_formulae_ L2 - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-S11-S6 DB - PRIME DP - Unbound Medicine ER -