reactome数据库更新啦

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

2102 pathways (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