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
更多套路，后台留言获取。