Identification of human gene core promoters in silico.
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Summary
Using positional dependent 5-tuple measures, a quadratic discriminant analysis (QDA) method has been implemented in a new program-CorePromoter, and experiments indicate that when given a 1- to 2-kb extended promoter, CorePromoter will correctly localize the TSS to a 100-bp interval approximately 60% of the time.
- Type
- article
- Published
- 1998-03-01
- Cited by
- 119
- References
- 22
- Access
- Open access
- OpenAlex
- https://openalex.org/W2114332734
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1039889
Keywords
In silico, Biology, Promoter, Identification (biology), Computational biology
References
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- The role of general initiation factors in transcription by RNA polymerase II.
- Compilation and analysis of eukaryotic POL II promoter sequences.
- RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box.
- A Conserved Downstream Element Defines a New Class of RNA Polymerase II Promoters (*)
- Predicting Pol II promoter sequences using transcription factor binding sites.
- Identification of protein coding regions in the human genome by quadratic discriminant analysis.
- The biochemistry of transcription in eukaryotes: a paradigm for multisubunit regulatory complexes.
- Statistical features of human exons and their flanking regions.
- The prediction of vertebrate promoter regions using differential hexamer frequency analysis
- The calculation of posterior distributions by data augmentation
- Computational methods for the identification of genes in vertebrate genomic sequences.
- The general transcription factors of RNA polymerase II.
- Eukaryotic promoter recognition.
- Discriminant Analysis and Statistical Pattern Recognition
- Site-Specific Initiation of Transcription by RNA Polymerase II
Cited by
- Finding and Decrypting of Promoters Contributes to the Elucidation of Gene Function
- Mammalian-wide interspersed repeats (MIRs) and their role in mammalian gene function and evolution
- Using CorePromoter to Find Human Core Promoters
- Using Amino Acid Patterns to Accurately Predict Translation Initiation Sites
- Computer System Gene Discovery for Promoter Structure Analysis
- An in-silico method for prediction of polyadenylation signals in human sequences.
- CUBIC: identification of regulatory binding sites through data clustering
- Using MZEF to Find Internal Coding Exons
- Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
- Osteo-Promoter Database (OPD) – Promoter analysis in skeletal cells
- Modification of hard-limiting multilayer neural networks for confidence evaluation
- IN-MACA-MCC: Integrated Multiple Attractor Cellular Automata with Modified Clonal Classifier for Human Protein Coding and Promoter Prediction
- Identification and analysis of eukaryotic promoters: recent computational approaches.
- Species differences in the induction and activation of the pregnane X receptor.
- Promoter prediction on a genomic scale--the Adh experience.
- Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1
- Computational approaches for deciphering the transcriptional regulatory network by promoter analysis
- Clustering and Detection of 5' Splice Sites of mRNA by k Weight-Matrices Model
- SP-transcription factors are involved in basal MVP promoter activity and its stimulation by HDAC inhibitors.
- In Silico Identification of Regulatory Elements of GRIN1 Genes
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