TCGA套路文章大全

一是直接找全局miRNA/mRNA表达对

• Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis 

GSE35982,BMC,2012

• Identifying microRNA/mRNA dysregulations in ovarian cancer 

TCGA,BMC,2012

• Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis 

(GSE11016,GSE12105,GSE16441,GSE23085),BMC,2013

• MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes. 

TCGA,Nat Commun. 2015

• Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer 

TCGA,PNAS,2013

• Crucial microRNAs and genes of human primary breast cancer explored by microRNA-mRNA integrated analysis 

GSE19783 ,Tumor Biology,2015

• Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs 

TCGA,PLOS ONE,2017

• Prediction of clinical outcome in glioblastoma using a biologically relevant nine-microRNA signature 

tcga,Molecular Oncology,2015

• Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

• Meta-analysis of microRNA expression in lung cancer 

GEO,International journal of cancer 2012

二是仅仅是针对感兴趣基因来分析公共数据

SAMSN1 Is Highly Expressed and Associated with a Poor Survival in Glioblastoma Multiforme(2013 PLOS ONE)

• Cancer-Testis Antigen Expression in Serous Endometrial Cancer with Loss of X Chromosome Inactivation]http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137476) 

TCGA,PLOS ONE,2014

• NTRK1 Fusion in Glioblastoma Multiforme 

TCGA,PLOS ONE,2014

• AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma 

(GSE 4271, GSE4412),PLOS ONE,2014

• Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma 

TCGA,PLOS ONE,2014

• Identification of MicroRNAs as Breast Cancer Prognosis Markers through the Cancer Genome Atlas 

TCGA,PLOS ONE,2016

• The mRNA related ceRNA–ceRNA landscape and significance across 20 major cancer types 

TCGA,Nucl Acids Res (2015)

• Genomic and Transcriptomic Alterations Associated with STAT3 Activation in Head and Neck Cancer 

TCGA,PLOS ONE,2016 

首先指明一个现象，多种癌症里面，尤其是HNSCC中，STAT3基因的第705个酪氨酸(Y,tyrosine)的磷酸化导致它被过度激活。 

所以，就针对STAT3基因抓取了HNSCC里面的各种关于它的数据：Mutation, mRNA expression, promoter methylation, and copy number alteration data were extracted from TCGA and examined in the context of pSTAT3(Y705) protein expression.从表达量的相关性找到了1279 相关genes

• A Seven-microRNA Expression Signature Predicts Survival in Hepatocellular Carcinoma 

TCGA，2015 PLOS ONE 

从题目就知道他们做了什么分析：In this study, the miRNA profiles in 327 HCC patients, including 327 tumor and 43 adjacent non-tumor tissues, from The Cancer Genome Atlas (TCGA) Liver hepatocellular carcinoma (LIHC) were analyzed.里面找到了差异的miRNA(Differentially expressed miRNAs (DEmiRNA) )，然后用了miRNA pathway analysis工具miRPath做了功能分析而已。当然，生存分析也必不可少啦。

• Integrative Subtype Discovery in Glioblastoma Using iCluster 

TCGA,2012 PLOS ONE 

这个稍微有点不同，作者用自己的2009年发表的iCluster工具来灌水，下载了TCGA glioblastoma (GBM)的3种数据，iCluster was applied using 1,599 copy number features, 1,515 DNA methylation features, and 1,740 expression features。用iCluster把GBM分成了3个亚型。还跟前人单纯的用表达数据，或者甲基化数据的分类做了比较，还跟PCA比较，必须是自己的好呀

• Integrated Multiple “-omics” Data Reveal Subtypes of Hepatocellular Carcinoma 

TCGA,2016 PLOS ONE 

用的是公共数据，用了多种数据来把样本分类，自己开发了一个简单粗糙的分类方法而已。

三是补充一点简单的实验，用TCGA数据做佐证而已。

WNT7A Regulation by miR-15b in Ovarian Cancer(2016 PLOS ONE)

miR-342 Regulates BRCA1 Expression through Modulation of ID4 in Breast Cancer( 2014 PLOS ONE)

Expression and Prognostic Value of Oct-4 in Astrocytic Brain Tumors(2016 PLOS ONE)

https://www.biomedcentral.com/search?query=TCGA

http://journals.plos.org/plosone/search?filterJournals=PLoSONE&q=tcga

http://www.nature.com/search?journal=srep&q=tcga

http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=search&op=advanced