Cancer数据库 | 数据集 | CRC | oncogene | tumor suppressor gene
大型Cancer数据库
- TCGA
- ICGC
目前已知的oncogene
什么是oncogene？跟其在癌症中的表达量无关，而是作用，主动去激发cancer的gene才算，这些基因正常情况下都是有自己作用的（proto-oncogene），被mutated/over-expressed之后才变为oncogene。
什么是tumor suppressor genes？anti-oncogene。主要是用于控制细胞正常生长，但无论如何变化都无法单独引发cancer，必须配合oncogene和environment才行，相当于分子层面的immune system。
TSGs can be grouped into the following categories: caretaker genes, gatekeeper genes, and more recently landscaper genes.
- 看守基因，Caretaker genes ensure stability of the genome via DNA repair and subsequently when mutated allow mutations to accumulate.[3]
- 看门基因，Meanwhile, gatekeeper genes directly regulate cell growth by either inhibiting cell cycle progression or inducing apoptosis.[3]
- 园丁基因，Lastly landscaper genes regulate growth by contributing to the surrounding environment, when mutated can cause an environment that promotes unregulated proliferation.
区别
An important difference between oncogenes and tumor suppressor genes is that oncogenes result from the activation (turning on) of proto-oncogenes,
but tumor suppressor genes cause cancer when they are inactivated (turned off).
对比
Oncogene
1. Mutation in one of the two alleles is sufficient for activity as an oncogene and often act dominant to wild type. 【显性mutantion】
2. Mutation often occurs in somatic tissues therefore not inherited 【体细胞突变，过早发生则直接致死】
3. Conversion of protooncogene to oncogene is often a “gain of function” of protein that signals uncontrolled cell division. 【GOF mutation】
4. Some tissue preference.
Tumor Suppressor Genes
1. Tumor suppressor gene malfunctioning is caused by mutations in both alleles or a mutation in one followed by a loss of or reduction to homozygosity in the second. 【隐性失活】
2. Mutation may occur in germ cell (can be inherited) or somatic cells. 【可遗传，比如APC导致的FAP】
3. ‘Loss of function’ mutation is the reason for tumor suppressor gene malfunctioning. 【LOF mutation】
4. Strong tissue preference in the case of mant tumor suppressor genes (Example: effect of RB II gene in retina) 【组织偏好】
我的解释
- oncogene，特指与癌症发生相关的基因，正常形态不致癌，只有在异常情况下（mutated or over-expressed）才导致癌症。
- 而TSG则是，平时也有正常功能，就是anti-oncogene，抑制癌症发生，一旦失活，接相当于解禁了，oncogene就能出来作妖了。
the first literature database for oncogenes
- 803 human oncogenes
- 8849 curated pubmed abstracts
OncoVar - 看这一个足以
- OncoVar is a platform to systematically prioritize the oncogenic ability of somatic mutations and cancer genes.
- 20,162 cancer driver mutations, 814 driver genes and 2,360 pathogenic pathways
- Data sources used in OncoVar - 良心总结
- 看看文章：2020 - NAR - OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers 【数据挖掘基本功】
GRNdb数据库 - 不太有用
