Welcome to dreamBase!


dreamBase (DNA Modification, RNA Regulation and Protein Binding on Expressed Pseudogenes in Human Health and Disease) is an integrated platform for analysing regualtory features of pseudogenes from multi-dimensional high-throughput sequencing data.

Based on ~5500 ChIP-seq and DNase-seq data, dreamBase provides genome-wide distribution patterns of Transcription Factors, Pol II, Histone Modifications and Dnase Hypersensitivity sites around the transcription start sites of pseudognenes.

By integrating ~18,000 RNA-Seq expression data, we provide the Expression Profiles of pseudogenes across 32 Cancers and 31 Normal Tissues. We also analyse the Co-Expression patterns between pseudogenes and their parent genes.

Through combining predicted binding sites of microRNAs with AGO CLIP-seq data, we study the relevance of microRNAs against RNA molecules of pseudogenes at post-transcriptional level. Besides, we combine these interaction and expression data of pseudogenes, and therefore construct ceRNA networks consisted of pseudogenes and other RNAs.

Ground on CLIP-seq data, we provide thousands of binding sites of RNA Binding Proteins on pseudogenes. We also provide the transcriptome-wide profiling of RNA Modifications on expressed pseudogenes based on epitranscriptome sequencing technologies. In addition, we provide a powerful dreamBase genome browser to visualize the distributions of these high-throughput sequencing data on pseudogenes.

How to cite:

dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. Zheng LL*, Zhou KR, Liu S, Zhang DY, Wang ZL, Chen ZR, Yang JH*, Qu LH*. Nucleic Acids Res. 2018 Jan 4;46(D1):D85-D91.

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Useful Tools

  Active Promoter

Investigate transcription factor bindings around pseudogenes

  Expression

Evaluate the expression of pseudogenes in multiple tissue and cell-lines

  microRNA

Investigate microRNA bindings on pseudogenes

  Modifications

Identify RNA modifications on pseudogenes

  coExp-pseudo

Explore Co-Expression patterns between pseudogenes and their parent genes

  CeRNA-pseudo

Explore ceRNA networks of pseudogenes, microRNAs and other RNAs.

  Genome Browser

Visualize the distributions of these high-throughput sequencing data on genome