Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
复制标题
研究结直肠癌中的 MicroRNA 和转录因子共调控网络
DOI：
10.1186/s12859-017-1796-4
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发表时间：
2017-09-02
影响因子：
3
通讯作者：
Zhang Q
中科院分区：
文献类型：
--
作者：
Wang H;Luo J;Liu C;Niu H;Wang J;Liu Q;Zhao Z;Xu H;Ding Y;Sun J;Zhang Q
BackgroundColorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through targeting critical genes in cellular system. However, it is unclear about which miRNAs play central roles in CRC’s pathogenesis and how they interact with transcription factors (TFs) to regulate the cancer-related genes.ResultsTo address this issue, we systematically explored the major regulation motifs, namely feed-forward loops (FFLs), that consist of miRNAs, TFs and CRC-related genes through the construction of a miRNA-TF regulatory network in CRC. First, we compiled CRC-related miRNAs, CRC-related genes, and human TFs from multiple data sources. Second, we identified 13,123 3-node FFLs including 25 miRNA-FFLs, 13,005 TF-FFLs and 93 composite-FFLs, and merged the 3-node FFLs to construct a CRC-related regulatory network. The network consists of three types of regulatory subnetworks (SNWs): miRNA-SNW, TF-SNW, and composite-SNW. To enhance the accuracy of the network, the results were filtered by using The Cancer Genome Atlas (TCGA) expression data in CRC, whereby we generated a core regulatory network consisting of 58 significant FFLs. We then applied a hub identification strategy to the significant FFLs and found 5 significant components, including two miRNAs (hsa-miR-25 and hsa-miR-31), two genes (ADAMTSL3andAXIN1) and one TF (BRCA1). The follow up prognosis analysis indicated all of the 5 significant components having good prediction of overall survival of CRC patients.ConclusionsIn summary, we generated a CRC-specific miRNA-TF regulatory network, which is helpful to understand the complex CRC regulatory mechanisms and guide clinical treatment. The discovered 5 regulators might have critical roles in CRC pathogenesis and warrant future investigation.
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影响因子：
64.8
作者：
Lu, J;Getz, G;Golub, TR
通讯作者：
Golub, TR
影响因子：
4.3
作者：
Langfelder P;Luo R;Oldham MC;Horvath S
通讯作者：
Horvath S
TransFac及其模块移植：真核生物中的转录基因调节。
影响因子：
14.9
作者：
Matys V;Kel-Margoulis OV;Fricke E;Liebich I;Land S;Barre-Dirrie A;Reuter I;Chekmenev D;Krull M;Hornischer K;Voss N;Stegmaier P;Lewicki-Potapov B;Saxel H;Kel AE;Wingender E
通讯作者：
Wingender E
可重复的组合调控网络阐明了非小细胞肺癌中新型致癌 microRNA。
DOI：
10.1261/rna.042754.113
发表时间：
2014-09
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Mitra R;Edmonds MD;Sun J;Zhao M;Yu H;Eischen CM;Zhao Z
通讯作者：
Zhao Z
影响因子：
5.2
作者：
Akcakaya, Pinar;Ekelund, Susanne;Lui, Weng-Onn
通讯作者：
Lui, Weng-Onn