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GO/Pathway 数据筛选
GO功能分析
一、显著性筛选
显著性P值
采用Fisher精确检验，对功能分析结果的显著性判断，一般选择P<0.05的功能为具有显著统计学意义的功能。
显著性FDR值
为了控制多重比较检验中犯第一类错误的整体概率，我们通过Benjamini-Hochberg step-up的方法来控制FDR，即判断为显著性的GO中假阳性GO的比例的期望，一般选择FDR<0.05是较为理想的结果，表示对应的功能具有显著统计学意义。
参考文献：
[1] Y. Benjamini, Y. Hochberg(1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57 (1): 289–300.
二、自定义筛选
关注的基因/关键字
根据用户关注的基因或功能名称中包含的关键字进行筛选，可同时输入多个基因/关键字。
信号通路（Pathway）分析
一、显著性筛选
显著性P值
采用Fisher精确检验，对通路分析结果的显著性判断，一般选择P<0.05的通路为具有显著统计学意义。
显著性FDR值
为了控制多重比较检验中犯第一类错误的整体概率，我们通过Benjamini-Hochberg step-up的方法来控制FDR，即判断为显著性的Pathway中假阳性Pathway的比例的期望，一般选择FDR<0.05是较为理想的结果，表示对应的通路具有显著统计学意义。
参考文献：
[1] Y. Benjamini, Y. Hochberg(1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57 (1): 289–300.
二、通路分类筛选
根据KEGG中常见的Immune system、Signal transduction、Cell growth and death、Endocrine system信号通路分类以及已报道的与肿瘤发生相关的信号通路，通过对每一信号通路包含的基因进行计数，用户可以根据关注的信号通路进行筛选。每一大类包含的信号通路如下：
| 与肿瘤相关的信号通路 | 与免疫相关的信号通路 | 与信号传导相关的信号通路 | 与内分泌系统相关的信号通路 | 与细胞周期相关的信号通路 |
| AMPK signaling pathway | Hematopoietic cell lineage | Two-component system | Insulin secretion | Cell cycle |
| Apoptosis | Complement and coagulation cascades | Ras signaling pathway | Insulin signaling pathway | Oocyte meiosis |
| B cell receptor signaling pathway | Platelet activation | Rap1 signaling pathway | Glucagon signaling pathway | Apoptosis |
| cAMP signaling pathway | Toll-like receptor signaling pathway | MAPK signaling pathway | Regulation of lipolysis in adipocytes | p53 signaling pathway |
| Cell cycle | Toll and Imd signaling pathway | ErbB signaling pathway | Adipocytokine signaling pathway | |
| Chemokine signaling pathway | NOD-like receptor signaling pathway | Wnt signaling pathway | PPAR signaling pathway | |
| Cytokine-cytokine receptor interaction | RIG-I-like receptor signaling pathway | Notch signaling pathway | GnRH signaling pathway | |
| HIF-1 signaling pathway | Cytosolic DNA-sensing pathway | Hedgehog signaling pathway | Ovarian steroidogenesis | |
| Hippo signaling pathway | Natural killer cell mediated cytotoxicity | TGF-beta signaling pathway | Estrogen signaling pathway | |
| Jak-STAT signaling pathway | Antigen processing and presentation | Hippo signaling pathway | Progesterone-mediated oocyte maturation | |
| MAPK signaling pathway | T cell receptor signaling pathway | VEGF signaling pathway | Prolactin signaling pathway | |
| mTOR signaling pathway | Th1 and Th2 cell differentiation | Apelin signaling pathway | Oxytocin signaling pathway | |
| NF-kappa B signaling pathway | Th17 cell differentiation New! | Jak-STAT signaling pathway | Thyroid hormone synthesis | |
| p53 signaling pathway | IL-17 signaling pathway New! | NF-kappa B signaling pathway | Thyroid hormone signaling pathway | |
| PI3K-Akt signaling pathway | B cell receptor signaling pathway | TNF signaling pathway | Melanogenesis | |
| T cell receptor signaling pathway | Fc epsilon RI signaling pathway | HIF-1 signaling pathway | Renin secretion | |
| TGF-beta signaling pathway | Fc gamma R-mediated phagocytosis | FoxO signaling pathway | Renin-angiotensin system | |
| Toll-like receptor signaling pathway | Leukocyte transendothelial migration | Calcium signaling pathway | Aldosterone synthesis and secretion | |
| VEGF signaling pathway | Intestinal immune network for IgA production | Phosphatidylinositol signaling system | ||
| Wnt signaling pathway | Chemokine signaling pathway | Phospholipase D signaling pathway | ||
| Sphingolipid signaling pathway | ||||
| cAMP signaling pathway | ||||
| cGMP-PKG signaling pathway | ||||
| PI3K-Akt signaling pathway | ||||
| AMPK signaling pathway | ||||
| mTOR signaling pathway | ||||
| Plant hormone signal transduction | ||||
三、自定义筛选
关注的基因/关键字
根据用户关注的基因或功能名称中包含的关键字进行筛选，可同时输入多个基因/关键字。
信号通路分类
根据KEGG数据库中信号通路的七大分类，分别对每一大类包含的信号通路进行数量统计，用户可以根据关注的研究方向进行筛选，7大分类如下：
| Category | 含义 |
| Metabolism | 属于代谢类的信号通路数量 |
| Genetic Information Processing | 属于转录、翻译、DNA修复等遗传信息传递类的信号通路数量 |
| Environmental Information Processing | 属于跨膜运输、信号传导等细胞间信息处理类的信号通路数量 |
| Cellular Processes | 属于细胞运输、生长等生物学过程的信号通路数量 |
| Organismal Systems | 属于免疫、内分泌、神经系统等机体系统类的信号通路数量 |
| Human Diseases | 属于疾病类的信号通路数量 |
| Drug Development | 属于药物作用、功能分类相关的信号通路数量 |
详细分类关系请可参照KEGG官网http://www.kegg.jp/kegg/pathway.html。
本文由 GCBI学院 作者：Lina 发表，转载请注明来源！
Lina
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