ReviewHuman molecular genetics2010
Transcribed dark matter: meaning or myth?
Review in Human molecular genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
163 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The Prognostic Value and Clinical Significance of lncRNA SNHG5 Expression in Patients with Multiple Malignancies: A Bioinformatic and Meta-analysis.Current cancer drug targets · 2024Pooled it
- The Effect of LINC01296 Expression in Patients with Cancer: A Systematic Review and Meta-Analysis.Asian Pacific journal of cancer prevention : APJCP · 2020Pooled it
- Genome-Scale Expression Pattern of Long Non-Coding RNAs in Chinese Uyghur Patients with Parkinson's Disease.Medical science monitor : international medical journal of experimental and clinical research · 2020Trial
- Non-Coding Transcripts From Diversified Members of IgLec Family Protect Antiviral Effectors From Viral miRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification of lncRNAs in Breast Cancer Through Bioinformatics Analysis: Implications for Pathogenesis and Prognostic Significance.Cancer medicine · 2026Article
- Application of RNA markers in forensic body fluid analysis: from specificity and stability to polymorphism.International journal of legal medicine · 2026Review
- Upregulation of the HOXA10-AS1 LncRNA in Gastric Cancer: An Expression and Bioinformatics Analysis.Iranian journal of pathology · 2026Article
- Article
- Hidden regulators: the emerging roles of lncRNAs in brain development and disease.Frontiers in neuroscience · 2024Review
- Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations.Journal of autoimmunity · 2023Review
- Expression of long noncoding RNAs in the ovarian granulosa cells of women with diminished ovarian reserve using high-throughput sequencing.Journal of ovarian research · 2022Article
- LncRNA HOXA10-AS functions as an oncogene by binding miR-6509-5p to upregulate Y-box binding protein 1 in gastric cancer.Bioengineered · 2022Article
- Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs.Non-coding RNA · 2022Review
- Functions of non-coding RNAs in regulating cancer drug targets.Acta biochimica et biophysica Sinica · 2022Review
- Bidirectional lncRNA Transfer betweenInternational journal of molecular sciences · 2022Article
- Fertilization, Oocyte Activation, Calcium Release and Epigenetic Remodelling: Lessons From Cancer Models.Frontiers in cell and developmental biology · 2022Article
- Article
- LncRNA CASC2 inhibits lung adenocarcinoma progression through forming feedback loop with miR-21/p53 axis.The Kaohsiung journal of medical sciences · 2021Article
- Investigation of the lncRNABiomedicines · 2021Article
- There and Back Again: Hox Clusters Use Both DNA Strands.Journal of developmental biology · 2021Review
103 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Genomic tiling arrays, cDNA sequencing and, more recently, RNA-Seq have provided initial insights into the extent and depth of transcribed sequence across human and other genomes. These methods have led to greatly improved annotations of protein-coding genes, but have also identified transcription outside of annotated exons. One resultant issue that has aroused dispute is the balance of transcription of known exons against transcription outside of known exons. While non-genic 'dark matter' transcription was found by tiling arrays to be pervasive, it was seen to contribute only a small percentage of the polyadenylated transcriptome in some RNA-Seq experiments. This apparent contradiction has been compounded by a lack of clarity about what exactly constitutes a protein-coding gene. It remains unclear, for example, whether or not all transcripts that overlap on either strand within a genomic locus should be assigned to a single gene locus, including those that fail to share promoters, exons and splice junctions. The inability of tiling arrays and RNA-Seq to count transcripts, rather than exons or exon pairs, adds to these difficulties. While there is agreement that thousands of apparently non-coding loci are present outside of protein-coding genes in the human genome, there is vigorous debate of what constitutes evidence for their functionality. These issues will only be resolved upon the demonstration, or otherwise, that organismal or cellular phenotypes frequently result when non-coding RNA loci are disrupted.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.