ArticleDevelopmental biology2012
RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes.
Article in Developmental biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- High expression of SMARCA4 or SMARCA2 is frequently associated with an opposite prognosis in cancer.Scientific reports · 2018Pooled it
- Combined Analysis of Second- and Third-Generation Transcriptome Sequencing for Gene Characteristics and Identification of Key Splicing Variants in Wound Healing of Ganxi Goat Skin.Animals : an open access journal from MDPI · 2024Article
- Rare cases of a second recurrence of nephroblastoma with MLLT1 gene mutation: case report and literature review.Frontiers in oncology · 2024Article
- Comparative whole-genome transcriptome analysis in renal cell populations reveals high tissue specificity of MAPK/ERK targets in embryonic kidney.BMC biology · 2022Article
- Immune Checkpoint B7x (B7-H4/B7S1/VTCN1) is Over Expressed in Spontaneous Canine Bladder Cancer: The First Report and its Implications in a Preclinical Model.Bladder cancer (Amsterdam, Netherlands) · 2019Article
- Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer.PLoS genetics · 2018Article
- Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number.Kidney international · 2018Article
- Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf.Developmental biology · 2018Article
- Identification of Osr2 Transcriptional Target Genes in Palate Development.Journal of dental research · 2017Article
- Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.The Journal of experimental medicine · 2017Article
- TβRII Regulates the Proliferation of Metanephric Mesenchyme Cells through Six2 In Vitro.International journal of molecular sciences · 2017Article
- Bmp4-Msx1 signaling and Osr2 control tooth organogenesis through antagonistic regulation of secreted Wnt antagonists.Developmental biology · 2016Article
- Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases.Scientific reports · 2016Article
- A Shh-Foxf-Fgf18-Shh Molecular Circuit Regulating Palate Development.PLoS genetics · 2016Article
- MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours.Nature communications · 2015Article
- Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development.BMC developmental biology · 2015Article
- Whole transcriptome expression profiling of mouse limb tendon development by using RNA-seq.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2015Article
- Induction and patterning of the metanephric nephron.Seminars in cell & developmental biology · 2014Review
- Single cell dissection of early kidney development: multilineage priming.Development (Cambridge, England) · 2014Article
- Building an atlas of gene expression driving kidney development: pushing the limits of resolution.Pediatric nephrology (Berlin, Germany) · 2014Review
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
During kidney development the cap mesenchyme progenitor cells both self renew and differentiate into nephrons. The balance between renewal and differentiation determines the final nephron count, which is of considerable medical importance. An important goal is to create a precise genetic definition of the early differentiation of cap mesenchyme progenitors. We used RNA-Seq to transcriptional profile the cap mesenchyme progenitors and their first epithelial derivative, the renal vesicles. The results provide a global view of the changing gene expression program during this key period, defining expression levels for all transcription factors, growth factors, and receptors. The RNA-Seq was performed using two different biochemistries, with one examining only polyadenylated RNA and the other total RNA. This allowed the analysis of noncanonical transcripts, which for many genes were more abundant than standard exonic RNAs. Since a large fraction of enhancers are now known to be transcribed the results also provide global maps of potential enhancers. Further, the RNA-Seq data defined hundreds of novel splice patterns and large numbers of new genes. Particularly striking was the extensive sense/antisense transcription and changing RNA processing complexities of the Hox clusters.
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.