Reactome knowledgebase of human biological pathways and processes

Matthews, Lisa; Gopinath, Gopal; Gillespie, Marc; Caudy, Michael; Croft, David; Bono, Bernard de; Garapati, Phani V.; Hemish, Jill; Hermjakob, Henning; Jassal, Bijay; Kanapin, Alexander; Lewis, Suzanna; Mahajan, Shahana S.; May, Bruce; Schmidt, Esther; Västrik, Imre; Wu, Guanming; Birney, Ewan; Stein, Lincoln; D’Eustachio, Peter

doi:10.1093/nar/gkn863

Cited by 775 publications

(670 citation statements)

References 11 publications

Supporting

Mentioning

667

Contrasting

Unclassified

Order By: Relevance

“…The term can be extracted by acting with n, m| = 0|â npm on (19) or (21), and using orthogonality condition n, m|n , m ∝ δ n,n δ m,m where δ denote the Kronecker delta function.The orthogonality condition follows from (16) and (18).…”

Section: Notation Preliminariesmentioning

confidence: 99%

See 1 more Smart Citation

Multiparticle reaction noise characteristics

Konkoli

2011

Journal of Theoretical Biology

View full text Add to dashboard Cite

Section: Notation Preliminariesmentioning

confidence: 99%

“…[15] The exact value cannot be deduced from experiments. Furthermore, an inspection of the Reactome database [16] which contains information on human pathways indicates that multiparticle-like reactions in the cell are rather frequent. One can find records where the number of inputs k ranges from k = 2 towards very large values.…”

Section: Introductionmentioning

confidence: 99%

Multiparticle reaction noise characteristics

Konkoli

2011

Journal of Theoretical Biology

View full text Add to dashboard Cite

“…PPI data were imported from eight existing PPI databases, including the Human Annotated and Predicted Protein Interaction Database (HAPPI) [23] , Reactome [24] , Online Predicted Human Interaction Database (OPHID) [25] , InAct [26] , Human Protein Reference Database (HPRD) [27] , Molecular Interaction Database (MINT) [28] , Database of Interacting Proteins (DIP) [29] , and PDZBase [30] . Detailed information about these PPI databases is described in Supplementary Table S3.…”

Section: Protein-protein Interaction (Ppi) Datamentioning

confidence: 99%

Deciphering the pharmacological mechanism of the Chinese formula Huanglian-Jie-Du decoction in the treatment of ischemic stroke using a systems biology-based strategy

et al. 2015

View full text Add to dashboard Cite

Aim: Huanglian-Jie-Du decoction (HLJDD) is an important multiherb remedy in TCM, which is recently demonstrated to be effective to treat ischemic stroke. Here, we aimed to investigate the pharmacological mechanisms of HLJDD in the treatment of ischemic stroke using systems biology approaches. Methods: Putative targets of HLJDD were predicted using MetaDrug. An interaction network of putative HLJDD targets and known therapeutic targets for the treatment of ischemic stroke was then constructed, and candidate HLJDD targets were identified by calculating topological features, including 'Degree', 'Node-betweenness', 'Closeness', and 'K-coreness'. The binding efficiencies of the candidate HLJDD targets with the corresponding compositive compounds were further validated by a molecular docking simulation. Results: A total of 809 putative targets were obtained for 168 compositive compounds in HLJDD. Additionally, 39 putative targets were common to all four herbs of HLJDD. Next, 49 major nodes were identified as candidate HLJDD targets due to their network topological importance. The enrichment analysis based on the Gene Ontology (GO) annotation system and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway demonstrated that candidate HLJDD targets were more frequently involved in G-protein-coupled receptor signaling pathways, neuroactive ligand-receptor interactions and gap junctions, which all played important roles in the progression of ischemic stroke. Finally, the molecular docking simulation showed that 170 pairs of chemical components and candidate HLJDD targets had strong binding efficiencies. Conclusion: This study has developed for the first time a comprehensive systems approach integrating drug target prediction, network analysis and molecular docking simulation to reveal the relationships between the herbs contained in HLJDD and their putative targets and ischemic stroke-related pathways.

show abstract

“…By using these databases alongside the iHOP website, we can construct the pathway map of interest, which is also referred to as an activity flow diagram (Figure 2b). Alternatively, repositories of already established maps are available through knowledge bases such as REACTOME [26], KEGG [24,27] and PANTHER [28], although these repositories do not necessarily cover all physiological events.…”

Section: Preparation Of Pathway Mapsmentioning

confidence: 99%

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

Kariya

Honma

Suzuki

2013

Biopharm & Drug Disp

View full text Add to dashboard Cite

The importance of systems-based pharmacological approaches to drug discovery and development has increasingly been recognized. This reviews summarizes recent advances in the development of systems pharmacology and introduces the methods used for analysis. To understand the cellular response at the molecular level, pathway maps must be prepared to show how the function of the constituent molecules within cells are linked and integrated to form molecular networks. First, the methods used to prepare these pathway maps, such as databases, knowledge bases and software platforms, are introduced. Then the mathematical theories used to analyse the behavior of molecular networks are summarized. To quantitatively predict cellular responses, simulations are performed that are based on the rate equations for each reaction within the pathway map. If the number of reactions described in the pathway map is small, and if the parameter values for the rate constants are available, it is possible accurately to simulate the behavior of the molecular networks. However, to analyse complex maps, mathematical abstraction is required. Such abstraction methods are important to integrate cellular responses and to understand tissue/organ and in vivo pharmacological/toxicological responses. The scope and limitations of the methods are also discussed.

show abstract

Reactome knowledgebase of human biological pathways and processes

Cited by 775 publications

References 11 publications

Multiparticle reaction noise characteristics

Multiparticle reaction noise characteristics

Deciphering the pharmacological mechanism of the Chinese formula Huanglian-Jie-Du decoction in the treatment of ischemic stroke using a systems biology-based strategy

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

Contact Info

Product

Resources

About