发表在 Nucleic Acids Research, January 2018, , https://doi.org/10.1093/nar/gkx1132
已有的同类数据库不少，比如： KEGG (2), MetaCyc (3) or PANTHER 但是 Reactome是唯一一个人工整理的，仅仅是针对于人类研究的。最新版 (version 62—September 2017) has entries for 10 719 human genes, 53% of the 20 338 predicted human protein-coding genes (http://www.ensembl.org/Homo_sapiens/Info/Annotation),
事实上，最新版是 ： Version 64 released on March 26, 2018
- (e.g. Interleukin-15 signaling; ) grouped into 26 superpathways
- 1334 mutant variants and their post-translationally modified forms derived from 285 gene products, used to annotate 906 disease-specific reactions, tagged with 294 Disease Ontology terms
- 1768 small molecules as substrates, catalysts, and regulators in 11 302 reactions annotated on the basis of data from 27 526 literature references
https://reactome.org/download/current/TheReactomeBook.pdf.zip 171Mb的PDF文件，超过两万页的知识。
开放下载
The Reactome graph database is freely available at: https://reactome.org/dev/graph-database. The API for the ContentService is available at https://reactome.org/ContentService with documentation and tutorials available at: https://reactome.org/dev/content-service. The Java source code is freely available at: https://github.com/reactome in the graph-core, graph-importer and content-service repositories.
网络学习资源
Reactome online resources
| Home page | https://reactome.org |
|---|---|
| an introductory video for users | https://youtu.be/-skixrvI4nU |
| The Reactome graph database | https://reactome.org/dev/graph-database |
| API for the ContentService | https://reactome.org/ContentService |
| documentation and tutorials | https://reactome.org/dev/content-service |
| Java source code | https://github.com/reactome |
| includes graph-core, graph-importer, content-service and analysis-tools repositories | |
| EHLD source code | https://github.com/reactome-pwp/diagram |
| reusable stand-alone JavaScript EHLD viewer | https://reactome.org/dev/diagram/js |
| EHLD icon library | https://reactome.org/icon-lib |
| community contributions to the library | https://reactome.org/icon-info |
简单探索
下载 https://reactome.org/download/current/NCBI2Reactome.txt 文件，看了看物种分布：
10788 Arabidopsis thaliana 16811 Bos taurus 9848 Caenorhabditis elegans 14850 Canis familiaris 19381 Danio rerio 4353 Dictyostelium discoideum 15820 Drosophila melanogaster 13977 Gallus gallus 40404 Homo sapiens 27359 Mus musculus 40 Mycobacterium tuberculosis 9054 Oryza sativa 1774 Plasmodium falciparum 22109 Rattus norvegicus 5116 Saccharomyces cerevisiae 3896 Schizosaccharomyces pombe 12573 Sus scrofa 3459 Taeniopygia guttata 7864 Xenopus tropicalis
在人类里面记录了 1772 个通路。
有一些通路基因比较多，也有一些通路甚至只有一个基因。
479 Neutrophil degranulation 392 Olfactory Signaling Pathway 343 Generic Transcription Pathway 310 Antigen processing: Ubiquitination & Proteasome degradation 266 G alpha (i) signalling events 235 Neddylation 220 Ub-specific processing proteases 207 SRP-dependent cotranslational protein targeting to membrane 206 HATs acetylate histones 190 Separation of Sister Chromatids 1 TALDO1 deficiency: failed conversion of SH7P, GA3P to Fru(6)P, E4P 1 Tandem pore domain halothane-inhibited K+ channel (THIK) 1 TLR3 deficiency - HSE 1 Toll Like Receptor 10 (TLR10) Cascade 1 Transport of connexons to the plasma membrane 1 TWIK-related spinal cord K+ channel (TRESK) 1 Variant SLC6A14 may confer susceptibility towards obesity 1 Vitamin E 1 WNT ligand secretion is abrogated by the PORCN inhibitor LGK974 1 ZBP1(DAI) mediated induction of type I IFNs