ArticleGenome research2001
Identification and characterization of the potential promoter regions of 1031 kinds of human genes.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 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
90 citing papers in PubMed, 250 citations in OpenAlex.
- Epigenome editing-mediated restoration ofBiochemistry and biophysics reports · 2025Article
- GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte.The Plant journal : for cell and molecular biology · 2025Article
- Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle.Biomolecules · 2024Review
- Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- NFκB (RelA) mediates transactivation of hnRNPD in oral cancer cells.Scientific reports · 2022Article
- Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding.Current issues in molecular biology · 2022Article
- Characterization of Genetic Variants in the SLC5A5 Gene and Associations With Breast Milk Iodine Concentration in Lactating Women of African Descent: The NUPED Study.Frontiers in nutrition · 2021Article
- Functional Analysis of Nuclear Factor Y in the Wing-Dimorphic Brown Planthopper,Frontiers in genetics · 2020Article
- ETS1 and SP1 drive DHX15 expression in acute lymphoblastic leukaemia.Journal of cellular and molecular medicine · 2018Article
- Modeling the Function of TATA Box Binding Protein in Transcriptional Changes Induced by HIV-1 Tat in Innate Immune Cells and the Effect of Methamphetamine Exposure.Frontiers in immunology · 2018Article
- Establishment of DNA methylation patterns of the Fibrillin1 (FBN1) gene in porcine embryos and tissues.The Journal of reproduction and development · 2017Article
- Insights into a key sulfite scavenger enzyme sulfite oxidase (Physiology and molecular biology of plants : an international journal of functional plant biology · 2017Article
- Involvement of DNA methylation in regulating rat Prop1 gene expression during pituitary organogenesis.The Journal of reproduction and development · 2017Article
- Article
- Maximal Expression of the Evolutionarily Conserved Slit2 Gene Promoter Requires Sp1.Cellular and molecular neurobiology · 2016Article
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
- Characterization of gene expression in mouse embryos at the 1-cell stage.The Journal of reproduction and development · 2016Article
- Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.Genome research · 2016Article
- Constitutive overexpression of the TaNF-YB4 gene in transgenic wheat significantly improves grain yield.Journal of experimental botany · 2015Article
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
15 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/Inr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.
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.