BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine
Zhongyang Liu,Feifei Guo,Yong Wang,Chun Li,Xinlei Zhang,Honglei Li,Lihong Diao,Jiangyong Gu,Wei Wang,Dong Li,Fuchu He +10 more
Reads0
Chats0
TLDR
BATMAN-TCM will contribute to the understanding of the “multi-component, multi-target and multi-pathway” combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCm’s molecular mechanism.Abstract:
Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM's diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ's cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the "multi-component, multi-target and multi-pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.read more
Citations
More filters
Journal ArticleDOI
TCMID 2.0: a comprehensive resource for TCM
TL;DR: With the significant increase of data, TCMID 2.0 will further facilitate TCM’s modernization and enhance the exploration of underlying biological processes that are response to the diverse pharmacologic actions of TCM.
Journal ArticleDOI
TCM network pharmacology: A new trend towards combining computational, experimental and clinical approaches.
TL;DR: Wang et al. as discussed by the authors introduced new progresses of TCM network pharmacology in recent years, including predicting herb targets, understanding biological foundation of diseases and syndromes, network regulation mechanisms of herbal formulae, and identifying disease and syndrome biomarkers based on biological network.
Journal ArticleDOI
Traditional Chinese Medicine (TCM) in the treatment of COVID-19 and other viral infections: Efficacies and mechanisms.
TL;DR: Wang et al. as mentioned in this paper discussed principles of TCM in curing infectious disease, and clinical evidence and mechanisms of the 6 most effective TCM recipes used in treating COVID-19 in 92% of all of the confirmed cases in China.
Journal ArticleDOI
The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology
TL;DR: Overall, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was the most frequently employed network pharmacology database in THM-NP studies.
Journal ArticleDOI
Protection against COVID-19 injury by qingfei paidu decoction via anti-viral, anti-inflammatory activity and metabolic programming.
Jian Chen,Yong-kui Wang,Yuan Gao,Ling-San Hu,Jiang-wei Yang,Jian-ru Wang,Wen-jie Sun,Zhi-Qiang Liang,Ye-min Cao,Cao Yongbing +9 more
TL;DR: QFPD had a protection effect on COVID-19 by regulating a complex molecular network with safety and efficacy, and part of the mechanism was associated with the regulation of anti-viral, anti-inflammatory activity and metabolic programming.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Open Babel: An open chemical toolbox
Noel M. O'Boyle,Michael Banck,Craig A. James,Chris Morley,Tim Vandermeersch,Geoffrey R. Hutchison +5 more
TL;DR: The implementation of Open Babel is detailed, key advances in the 2.3 release are described, and a variety of uses are outlined both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Related Papers (5)
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
DrugBank 5.0: a major update to the DrugBank database for 2018
David S. Wishart,Yannick Djoumbou Feunang,An Chi Guo,Elvis J. Lo,Ana Marcu,Jason R. Grant,Tanvir Sajed,Daniel Johnson,Carin Li,Zinat Sayeeda,Nazanin Assempour,Ithayavani Iynkkaran,Yifeng Liu,Adam Maciejewski,Nicola Gale,Alex Wilson,Lucy Chin,Ryan Cummings,Diana Le,Allison Pon,Craig Knox,Michael Wilson +21 more