Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers
文献类型：期刊论文
| 作者 | Yan, ZY; Shah, PK; Amin, SB; Samur, MK; Huang, N; Wang, XJ; Misra, V; Ji, HB; Gabuzda, D; Li, C |
| 刊名 | NUCLEIC ACIDS RESEARCH
 |
| 出版日期 | 2012 |
| 卷号 | 40期号:17页码:e135-e135 |
| 通讯作者 | Li, C (reprint author), Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02215 USA.,cli@hsph.harvard.edu |
| 英文摘要 | We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted FFLs by their explanatory power to account for differential gene and miRNA expression between two biological conditions such as normal and cancer. GemiNI integrates not only gene and miRNA expression data but also computationally derived information about TF-target gene and miRNA-mRNA interactions. Literature validation shows that the integrated modeling of expression data and FFLs better identifies cancer-related TFs and miRNAs compared to existing approaches. We have utilized GemiNI for analyzing six data sets of solid cancers (liver, kidney, prostate, lung and germ cell) and found that top-ranked FFLs account for similar to 20% of transcriptome changes between normal and cancer. We have identified common FFL regulators across multiple cancer types, such as known FFLs consisting of MYC and miR-15/miR-17 families, and novel FFLs consisting of ARNT, CREB1 and their miRNA partners. The results and analysis web server are available at ext-link-type="uri" xlink:href="http://www.canevolve.org/dChip-GemiNi" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.canevolve.org/dChip-GemiNi. |
| 学科主题 | Biochemistry & Molecular Biology |
| 类目[WOS] | Biochemistry & Molecular Biology |
| 关键词[WOS] | MESSENGER-RNA TARGETS ; LUNG-CANCER ; HEPATOCELLULAR-CARCINOMA ; MICRORNA ; NETWORK ; PROTEIN ; MYC ; PROGNOSIS ; CIRCUITS ; ONCOMIRS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000309464300009 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/676]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Yan, ZY,Shah, PK,Amin, SB,et al. Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers[J]. NUCLEIC ACIDS RESEARCH,2012,40(17):e135-e135. |
| APA | Yan, ZY.,Shah, PK.,Amin, SB.,Samur, MK.,Huang, N.,...&Li, C.(2012).Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers.NUCLEIC ACIDS RESEARCH,40(17),e135-e135. |
| MLA | Yan, ZY,et al."Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers".NUCLEIC ACIDS RESEARCH 40.17(2012):e135-e135. |
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