SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
Jian Zhu,Michael Q. Zhang +1 more
- Vol. 15, Iss: 7, pp 607-611
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TLDR
A comprehensive yeast-specific promoter database that contains relevant binding affinity and expression data where available and provides some simple but useful tools for promoter sequence analysis is developed.Abstract:
MOTIVATION: In order to facilitate a systematic study of the promoters and transcriptionally regulatory cis-elements of the yeast Saccharomyces cerevisiae on a genomic scale, we have developed a comprehensive yeast-specific promoter database, SCPD. RESULTS: Currently SCPD contains 580 experimentally mapped transcription factor (TF) binding sites and 425 transcriptional start sites (TSS) as its primary data entries. It also contains relevant binding affinity and expression data where available. In addition to mechanisms for promoter information (including sequence) retrieval and a data submission form, SCPD also provides some simple but useful tools for promoter sequence analysis. AVAILABILITY: SCPD can be accessed from the URL http://cgsigma.cshl.org/jian. The database is continually updated.read more
Citations
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Book ChapterDOI
The probability distribution of distance TSS-TLS is organism characteristic and can be used for promoter prediction
Yun Dai,Ren Zhang,Yan-Xia Lin +2 more
TL;DR: In this article, the distance distribution between gene transcription and translation start sites (TSS-TLS) is used to test an assumption that over evolution, the TSS-Tls distance becomes a distinct character for a given organism.
Dissertation
Computational approaches for gene network discovery
TL;DR: The main contribution of this dissertation is a method that relies on a new machine learning approach called rule-based clustering that can combine regulatory DNA sequence and phenotype data to infer rules that describe clusters of genes with similar phenotype and regulatory structure.
Posted ContentDOI
Non-adaptive factors determine which equally effective regulatory motif evolves to generate pulses
TL;DR: The results suggest that evolutionary accessibility, and not relative functionality, shapes which motifs evolve in TRNs, and does so as a function of the expression levels of particular genes.
Journal ArticleDOI
Estimating motifs under order restrictions.
TL;DR: This work constrain the order of the information (entropy) in the columns of the position specific weight matrix (PWM) which characterizes the motif being sought and shows how to compute the maximum likelihood estimate of a PWM under such order restrictions.
Book ChapterDOI
Identifying binding sites in sequential genomic data
TL;DR: It is shown that using an SVM together with data sampling, to integrate the results of individual algorithms specialised for the prediction of binding site locations, can produce significant improvements upon the original algorithms.
References
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