ArticleNucleic acids research2003
SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed, 19 citations in OpenAlex.
- α-Synuclein induces alterations in adult neurogenesis in Parkinson disease models via p53-mediated repression of Notch1.The Journal of biological chemistry · 2012Article
- Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate.Methods (San Diego, Calif.) · 2009Article
- Functional roles for the striatal-enriched transcription factor, Bcl11b, in the control of striatal gene expression and transcriptional dysregulation in Huntington's disease.Neurobiology of disease · 2008Article
- Control of core 2 beta1,6 N-acetylglucosaminyltransferase-I transcription by Sp1 in lymphocytes and epithelial cells.Glycoconjugate journal · 2007Article
- FAST DB: a website resource for the study of the expression regulation of human gene products.Nucleic acids research · 2005Article
- POBO, transcription factor binding site verification with bootstrapping.Nucleic acids research · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The regulation of gene expression is a fundamental process within every living cell, which allows organisms to manage the precise levels of functional gene products with high sensitivity. It is well established that specific DNA sequences located upstream of the transcriptional start site are important in facilitating the binding of regulatory proteins that control the transcription of the gene. Indeed, microarray-based studies have successfully mined the upstream regions of co-expressed genes and discovered over-represented sequences corresponding to known promoter sites. Here we describe a tool for the visualisation of mapped transcription factor binding sites in the upstream regions of either single or grouped eukaryotic genes, which allows users to examine the positions of known and user-defined sites (http://rocky.bms.umist.ac.uk/SiteSeer/). SiteSeer allows the user to map different sections of the TRANSFAC and SCPD databases (or a set of user-defined sites) onto nucleotide sequences. Additionally, users may restrict the analysis by expectation values for certain DNA words as well as by known binding sites specific to a given organism. We believe this tool will prove particularly valuable for biologists who wish to examine sets of co-expressed or functionally-related genes and those who wish to visualise the positions of promoter sequences and generate displays for publications.
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.