利用TCGA发文章的那些套路

• 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
• 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

• 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。

接着针对STAT3基因，抓取HNSCC相关的数据：Mutation, mRNA expression, promoter methylation, and copy number alteration data were extracted from TCGA and examined in the context of pSTAT3(Y705) protein expression.

进而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.

找到了差异表达的miRNA(Differentially expressed miRNAs (DEmiRNA) )，然后用miRNA pathway analysis工具miRPath做了功能分析。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。

再与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。

• 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