ArticlePLoS genetics2006
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
Article in PLoS genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis 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
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Competing endogenous RNA (ceRNA) networks in Parkinson's disease: A systematic review.Frontiers in cellular neuroscience · 2023Pooled it
- Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing.International journal of molecular sciences · 2025Review
- The Role of Long Intergenic Noncoding RNA in Fetal Development.International journal of molecular sciences · 2024Review
- Importance of Studying Non-Coding RNA in Children and Adolescents with Type 1 Diabetes.Biomedicines · 2024Review
- Review
- An Integrated Approach for Microprotein Identification and Sequence Analysis.Journal of visualized experiments : JoVE · 2022Article
- Placenta-specific lncRNA 1600012P17Rik is expressed in spongiotrophoblast and glycogen trophoblast cells of mouse placenta.Histochemistry and cell biology · 2022Article
- Systematic Functional Annotation Workflow for Insects.Insects · 2022Article
- Non-coding antisense transcripts: fine regulation of gene expression in cancer.Computational and structural biotechnology journal · 2022Review
- Methods for the Study of Long Noncoding RNA in Cancer Cell Signaling.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Long Non-Coding RNAFrontiers in cell and developmental biology · 2021Article
- LINC00689 promotes prostate cancer progression via regulating miR-496/CTNNB1 to activate Wnt pathway.Cancer cell international · 2020Article
- Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response.BMC genomics · 2019Article
- Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved inInsects · 2019Article
- Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding.Nature protocols · 2019Article
- Article
- Shedding Light on the Dark Cancer Genomes: Long Noncoding RNAs as Novel Biomarkers and Potential Therapeutic Targets for Cancer.Molecular cancer therapeutics · 2018Review
- Landscape of long non-coding RNAs in Trichophyton mentagrophytes-induced rabbit dermatophytosis lesional skin and normal skin.Functional & integrative genomics · 2018Article
- Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.Genetics, selection, evolution : GSE · 2018Article
- The functions and unique features of long intergenic non-coding RNA.Nature reviews. Molecular cell biology · 2018Review
30 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
34 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.
Indexed as
Identifiers
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.