ArticleNucleic acids research2007
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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
14 citing papers in PubMed.
- Regulation of PLPP3 gene expression by NF-κB family transcription factors.The Journal of biological chemistry · 2019Article
- Neuronal apoptosis by HIV-1 Vpr: contribution of proinflammatory molecular networks from infected target cells.Journal of neuroinflammation · 2012Article
- Article
- KIT signaling regulates MITF expression through miRNAs in normal and malignant mast cell proliferation.Blood · 2011Article
- Long range regulation of human FXN gene expression.PloS one · 2011Article
- Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information.BMC medical genomics · 2010Article
- Transcription factor site dependencies in human, mouse and rat genomes.BMC bioinformatics · 2009Article
- Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene.EMBO molecular medicine · 2009Article
- Article
- An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer.BMC medical genomics · 2008Article
- Article
- Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis.Advances in genetics · 2008Review
- Characterization of microRNA expression profiles in normal human tissues.BMC genomics · 2007Article
- Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer.Genome biology · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource--GenomeTraFac (http://genometrafac.cchmc.org)--that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.
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.