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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

 

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本文由 GCBI学院 作者:Lina 发表,转载请注明来源!

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