Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences (Q34327872)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12136103%20AND%20SRC:MED&resulttype=core&format=json

11 November 2019

title

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences (English)

1 reference

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11 November 2019

0 references

1

1 reference

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11 November 2019

2

John L Spouge

1 reference

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11 November 2019

author name string

Ulla Hansen

series ordinal

3

1 reference

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11 November 2019

Zhiping Weng

series ordinal

4

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11 November 2019

language of work or name

English

0 references

publication date

1 July 2002

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11 November 2019

published in

Nucleic Acids Research

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11 November 2019

volume

30

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11 November 2019

issue

14

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11 November 2019

page(s)

3214-3224

1 reference

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Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

11 November 2019

cites work

1 reference

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The DNA sequence and comparative analysis of human chromosome 20

6 July 2018

1 reference

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Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

6 July 2018

1 reference

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DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs

6 July 2018

1 reference

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Detection of cis-element clusters in higher eukaryotic DNA.

6 July 2018

1 reference

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14-3-3tau associates with and activates the MEF2D transcription factor during muscle cell differentiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Nuclear hormone receptors and gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Sp1 and krüppel-like factor family of transcription factors in cell growth regulation and cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Adenylate kinase phosphotransfer communicates cellular energetic signals to ATP-sensitive potassium channels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Structure-function studies of ETS transcription factors.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identification and characterization of the potential promoter regions of 1031 kinds of human genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Initial sequencing and analysis of the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

The Sequence of the Human Genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Activation of the myocyte enhancer factor-2 transcription factor by calcium/calmodulin-dependent protein kinase-stimulated binding of 14-3-3 to histone deacetylase 5

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Adenylate kinase 1 gene deletion disrupts muscle energetic economy despite metabolic rearrangement

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

CART classification of human 5' UTR sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

GATA-4 and serum response factor regulate transcription of the muscle-specific carnitine palmitoyltransferase I beta in rat heart

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identification and characterization of a critical CP2-binding element in the human interleukin-4 promoter

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Inhibition of the mammalian transcription factor LSF induces S-phase-dependent apoptosis by downregulating thymidylate synthase expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A greedy algorithm for aligning DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

DNA binding sites: representation and discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

TRANSFAC: an integrated system for gene expression regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

The eukaryotic promoter database (EPD).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Tandem repeats finder: a program to analyze DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Transcription factor CP2 is essential for lens-specific expression of the chicken alphaA-crystallin gene.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identification of regulatory regions which confer muscle-specific gene expression.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Cloning and expression of human adenylate kinase 2 isozymes: differential expression of adenylate kinase 1 and 2 in human muscle tissues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Repression of human immunodeficiency virus type 1 through the novel cooperation of human factors YY1 and LSF

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

The hardwiring of development: organization and function of genomic regulatory systems.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Prediction of complete gene structures in human genomic DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A statistical model for locating regulatory regions in genomic DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Localization of Xenopus Vg1 mRNA by Vera protein and the endoplasmic reticulum.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Activation of the cardiac alpha-actin promoter depends upon serum response factor, Tinman homologue, Nkx-2.5, and intact serum response elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Tissue-specific and developmentally regulated expression of the genes encoding adenylate kinase isozymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Characterization of the molecularly cloned murine alpha-globin transcription factor CP2

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A novel LBP-1-mediated restriction of HIV-1 transcription at the level of elongation in vitro

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identification of common molecular subsequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Specific stimulation of simian virus 40 late transcription in vitro by a cellular factor binding the simian virus 40 21-base-pair repeat promoter element

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Identification of multiple proteins that interact with functional regions of the human cardiac alpha-actin promoter

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Methods for calculating the probabilities of finding patterns in sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Repression of HIV-1 transcription by a cellular protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Molecular cloning of the alpha-globin transcription factor CP2

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Activation of RNA polymerase II transcription by the specific DNA-binding protein LSF. Increased rate of binding of the basal promoter factor TFIIB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Promoter region-based classification of genes.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Human-mouse genome comparisons to locate regulatory sites

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Genomic sequence comparison of the human and mouse adenosine deaminase gene regions.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

The statistical significance of nucleotide position-weight matrix matches.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=135758

Transcriptional control elements and complex initiation pattern of the TATA-less bidirectional human thymidylate synthase promoter

27 October 2018

1 reference

12 December 2020

Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes

1 reference

12 December 2020

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

1 reference

12 December 2020

From Bioinformatics to Computational Biology

1 reference

12 December 2020

Compromised energetics in the adenylate kinase AK1 gene knockout heart under metabolic stress

1 reference

12 December 2020

Transcription factor LSF binds two variant bipartite sites within the SV40 late promoter

1 reference

12 December 2020

Striking sequence similarity over almost 100 kilobases of human and mouse T–cell receptor DNA

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKF438

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12136103%20AND%20SRC:MED&resulttype=core&format=json

11 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12136103%20AND%20SRC:MED&resulttype=core&format=json

11 November 2019

PubMed publication ID

12136103

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12136103%20AND%20SRC:MED&resulttype=core&format=json