TRED: a transcriptional regulatory element database, new entries and other development
By Cizhong Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang. Nucleic Acids Res., 2007
334 citations recorded by the source corpus.
Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED () was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF–target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7bf5493e4bdcb6705f8520788838bb9327e0bda3
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In Molecular Biology
Citations in the corpus
- RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, background): “For each type of the motifs, the Z-score is calculated as the difference of its actual occurrence frequency and the average of its occurrence frequencies in 100 random networks of the same node-size, normalized by the standard deviation of these random occurrence frequencies, and the motifs with a Z”
- A human functional protein interaction network and its application to cancer data analysis (2010, methodology): “To further increase the coverage of our network, we imported interactions between human transcription factors and their targets from the TRED database [64].”
- ConsensusPathDB—a database for integrating human functional interaction networks (2008, background): “…represented in our data-base (283 interactions) because on the one hand, such data are rare compared to other interaction types (e.g. protein– protein interactions), and, on the other hand, access to the majority of existing gene regulatory data is mostly limited by license constraints (28, 29).”