ArticleNucleic acids research2018
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 72 citations in OpenAlex.
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes.BMC genomic data · 2024Article
- A key regulatory loop AK4P1/miR-375/SP1 in pancreatic adenocarcinoma.Epigenetics · 2023Article
- Human VDAC pseudogenes: an emerging role for VDAC1P8 pseudogene in acute myeloid leukemia.Biological research · 2023Article
- Inferring pseudogene-MiRNA associations based on an ensemble learning framework with similarity kernel fusion.Scientific reports · 2023Article
- Shining a spotlight on m6A and the vital role of RNA modification in endometrial cancer: a review.Frontiers in genetics · 2023Review
- Article
- N6-methyladenosine-associated prognostic pseudogenes contribute to predicting immunotherapy benefits and therapeutic agents in head and neck squamous cell carcinoma.Theranostics · 2022Article
- Roles of ncRNAs as ceRNAs in Gastric Cancer.Genes · 2021Review
- Pseudogene ACTBP2 increases blood-brain barrier permeability by promoting KHDRBS2 transcription through recruitment of KMT2D/WDR5 in AβCell death discovery · 2021Article
- Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes.Genome biology · 2021Article
- Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens.Communications biology · 2021Article
- Predicting Pseudogene-miRNA Associations Based on Feature Fusion and Graph Auto-Encoder.Frontiers in genetics · 2021Review
- Pseudogenes: Four Decades of Discovery.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A Critical Role of Peptidylprolyl Isomerase A Pseudogene 22/microRNA-197-3p/Peptidylprolyl Isomerase A Axis in Hepatocellular Carcinoma.Frontiers in genetics · 2021Article
- Article
- lncRNA DUXAP8 Facilitates Multiple Malignant Phenotypes and Resistance to PARP Inhibitor in HCC via Upregulating FOXM1.Molecular therapy oncolytics · 2020Article
- Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation.Plant communications · 2020Review
- Pseudogene AKR1B10P1 enhances tumorigenicity and regulates epithelial-mesenchymal transition in hepatocellular carcinoma via stabilizing SOX4.Journal of cellular and molecular medicine · 2020Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.
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