seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
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seq-ImmuCC：组织转录组的以细胞为中心的视图，从小鼠 RNA-Seq 数据测量免疫微环境的细胞组成
DOI：
10.3389/fimmu.2018.01286
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发表时间：
2018
影响因子：
7.3
通讯作者：
Wu A
中科院分区：
文献类型：
--
作者：
Chen Z;Quan L;Huang A;Zhao Q;Yuan Y;Yuan X;Shen Q;Shang J;Ben Y;Qin FX;Wu A
RNA测序方法已被广泛用于为各种细胞和组织样品提供以基因、途径和网络为中心的分析。然而，到目前为止，组织样本中携带的丰富细胞信息尚未从RNA-Seq数据中彻底表征。因此，它将扩大我们的视野，以更好地了解身体的生物过程，通过纳入组织转录组的细胞为中心的观点。在这里，开发了一种名为seq-ImmuCC的计算模型，以从RNA-Seq数据推断小鼠组织中10种主要免疫细胞的相对比例。seq-ImmuCC的性能在多种计算算法、转录平台以及模拟和实验数据集之间进行了评估。测试结果表明，该系统性能稳定，在不同条件下与实验观测结果具有很好的一致性。使用seq-ImmuCC，我们生成了27个正常小鼠组织中免疫细胞组成的综合景观，并提取了不同组织类型中免疫细胞比例的独特特征。此外，我们定量表征和比较了18种不同类型的不同细胞来源的小鼠肿瘤组织及其免疫细胞组成，这为肿瘤组织内的免疫微环境提供了全面和信息性的测量。seq-ImmuCC的在线服务器可以免费获得。
The RNA sequencing approach has been broadly used to provide gene-, pathway-, and network-centric analyses for various cell and tissue samples. However, thus far, rich cellular information carried in tissue samples has not been thoroughly characterized from RNA-Seq data. Therefore, it would expand our horizons to better understand the biological processes of the body by incorporating a cell-centric view of tissue transcriptome. Here, a computational model named seq-ImmuCC was developed to infer the relative proportions of 10 major immune cells in mouse tissues from RNA-Seq data. The performance of seq-ImmuCC was evaluated among multiple computational algorithms, transcriptional platforms, and simulated and experimental datasets. The test results showed its stable performance and superb consistency with experimental observations under different conditions. With seq-ImmuCC, we generated the comprehensive landscape of immune cell compositions in 27 normal mouse tissues and extracted the distinct signatures of immune cell proportion among various tissue types. Furthermore, we quantitatively characterized and compared 18 different types of mouse tumor tissues of distinct cell origins with their immune cell compositions, which provided a comprehensive and informative measurement for the immune microenvironment inside tumor tissues. The online server of seq-ImmuCC are freely available at .
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影响因子：
7.7
作者：
Racle J;de Jonge K;Baumgaertner P;Speiser DE;Gfeller D
通讯作者：
Gfeller D
影响因子：
4.5
作者：
Odhams CA;Cunninghame Graham DS;Vyse TJ
通讯作者：
Vyse TJ
影响因子：
7
作者：
Shen-Orr SS;Gaujoux R
通讯作者：
Gaujoux R
影响因子：
12.3
作者：
Li B;Severson E;Pignon JC;Zhao H;Li T;Novak J;Jiang P;Shen H;Aster JC;Rodig S;Signoretti S;Liu JS;Liu XS
通讯作者：
Liu XS
影响因子：
8.8
作者：
Aguirre-Gamboa R;Joosten I;Urbano PCM;van der Molen RG;van Rijssen E;van Cranenbroek B;Oosting M;Smeekens S;Jaeger M;Zorro M;Withoff S;van Herwaarden AE;Sweep FCGJ;Netea RT;Swertz MA;Franke L;Xavier RJ;Joosten LAB;Netea MG;Wijmenga C;Kumar V;Li Y;Koenen HJPM
通讯作者：
Koenen HJPM