图1 真核有参转录组分析流程图

图2 原核有参转录组分析流程图

图3 原核链特异性全谱转录组分析流程图

经典案例

中国人群前列腺癌转录组研究检测到大量的基因融合及可变剪接 Cell Research. 2012. 

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Research. 2012, doi: 10.1038/cr.2012.30.

本文对来自14个患者的原发前列腺癌样本以及它们的正常组织对照样本进行了转录组测序及分析，分别对每个样本进行基因融合、差异表达lncRNA、可变剪接、SNP和Pathway富集分析，发现了大量的基因融合和可变剪接现象，并通过基因差异表达分析和Pathway富集分析，找到了前列腺癌中受影响的3大信号通路。

图1  前列腺癌中的基因融合现象。（A）14例样本中基因融合CIRCOS图。（B）TMPRSS2-ERG基因融合。（C）CTAGE5-KHDRBS3基因融合。（E）前列腺癌中TMPRSS2-ERG, USP9Y-TTTY15, CTAGE5-KHDRBS3, RAD50-PDLIM4, and SDK1-AMACR基因融合的比例。

图2  前列腺癌中的可变剪接现象。（A）14例样本中可变剪接CIRCOS图。（B）KLK3 (PSA)基因的可变剪接示意图。

图3  前列腺癌中被影响的3个信号通路。（A）RAS-PI3K-AKT通路。（B）AR通路。（C）RB通路。

推荐文献

[1] Minor class splicing shapes the zebrafish transcriptome during development. PNAS. 2014, doi: 10.1073/pnas. 1305536111.
[2] A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nature Communication. 2014, 5:3230. doi: 10.1038/ncomms4230.
[3] RNA sequencing reveals the complex regulatory network in the maize kernel. Nature Communication. 2013, 4:2832. doi: 10.1038/ncomms3832.
[4] Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca. The Plant Cell. 2013, doi: 10.1105/tpc.113.111732.
[5] Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology. 2012, doi:10.1038/nbt.2122.
[6] Genome-wide antisense transcription drives mRNA processing in bacteria. PNAS. 2011, doi/10.1073/pnas.1113521108.
[7] Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet. 2010, doi: 10.1038/nrg2695.