Characterizing and annotating the genome using RNA-seq data

Chen, Geng; Shi, Tieliu; Shi, Leming

doi:10.1007/s11427-015-0349-4

Cited by 41 publications

(21 citation statements)

References 63 publications

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“…In general, DNA methylation status is more reliable than gene expression in cancer diagnosis [1]. Over the past few years, it has been proved that aberrant DNAm plays a key role in diverse diseases [2][3][4], especially cancers [5]. It is generally believed that the promoter regions of tumor suppressor genes (TSGs) are hypermethylated and repressed, whereas oncogenes are hypomethylated and abnormally active in cancers cells [6].…”

Section: Introductionmentioning

confidence: 99%

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

2019

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DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.

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Section: Introductionmentioning

confidence: 99%

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

2019

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“…RNA deep sequencing (RNA-seq) is a widely used high-throughput genotyping method that measures the expression levels of thousands of coding and non-coding genes with high signal-to-noise ratio, high dynamic range, high reliability, and accuracy (Mortazavi et al 2008;Nagalakshmi et al 2010;Chen et al 2017). Considering that there remains great unknown about facet joint osteoarthritis, in the current study, we collected samples from healthy controls and patients with facet cartilage degeneration and performed RNA-seq.…”

Section: Introductionmentioning

confidence: 99%

Altered Wnt and NF-<i>κ</i>B Signaling in Facet Joint Osteoarthritis: Insights from RNA Deep Sequencing

Chu

Bao

et al. 2018

Tohoku J. Exp. Med.

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Facet joint osteoarthritis is common lumbar osteoarthritis characterized by facet joint cartilage degeneration. However, the molecular basis of facet joint osteoarthritis remains largely undetermined. In the current study, we collected facet joint tissue samples from 10 control patients and 48 patients with facet joint osteoarthritis (20 patients with moderate degeneration and 28 with severe degeneration). The control patients underwent internal fixation of the lumbar spine due to vertebral fracture. RNA deep sequencing was performed, and Bioinformatic tools were applied. Among top 30 enriched signaling pathways, we focused on two inflammation-related signaling pathways, Wnt and NF-κB signaling pathways. Subsequently, using the quantitative RT-PCR analysis, we confirmed that in Wnt signaling pathway, the mRNA levels of Dickkopf WNT Signaling Pathway Inhibitor 2 (DKK2), Sex-determining Region Y-box 17 (SOX17), MYC, Cyclin D1, Calcium/Calmodulin Dependent Protein Kinase II Alpha (CAMK2A), and Wnt Family Member 11 and 5 were increased in facet joint osteoarthritis, while the mRNA levels of WNT Inhibitory Factor 1, Casein Kinase 1 Alpha 1, Transcription Factor 7/Lymphoid Enhancer Binding Factor 1 (TCF7/LEF1), and VANGL Planar Cell Polarity Protein 2 were decreased. In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.

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“…[18] 和中黑盲蝽(Adelphocoris suturalis) [15] , 本文的测序结果在序列数量、平均长度、 N50等参数上有着更高的质量. 昆虫基因组测序近几年有了很大发展 [49] , 转录组可以用于基因组测序结果的优化 [50] , 为将来绿盲蝽基因组研究提供支撑. 此外, 转录组结果不仅提供了大量昆虫生理生化方面的信息, 也帮助孕育防治绿盲蝽的新思路和新方法, 例如, 利用miRNA [20] 和dsRNA [19] 对昆虫靶基因进行调控, 以及最近发展起来的基因编辑技术 [51] .…”

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