Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements (Q40414309)

20 September 2017

Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements (English)

1 reference

20 September 2017

cis-regulatory element

1 reference

1 reference

1

1 reference

20 September 2017

Panayiotis V Benos

8

0 references

Eleanor Feingold

object named as

Eleanor Feingold

2

0 references

author name string

Jessica Dominick

3

1 reference

20 September 2017

Marietta Wright

4

1 reference

20 September 2017

Jo Harnaha

5

1 reference

20 September 2017

Massimo Trucco

6

1 reference

20 September 2017

Nick Giannoukakis

7

1 reference

20 September 2017

1 June 2005

1 reference

20 September 2017

1 reference

20 September 2017

15

1 reference

20 September 2017

6

1 reference

20 September 2017

840-847

1 reference

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

20 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

enoLOGOS: a versatile web tool for energy normalized sequence logos

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Peroxide-mediated chromatin remodelling of a nuclear factor kappaB site in the mouse inducible nitric oxide synthase promoter

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Genetic analysis of NF- B/Rel transcription factors defines functional specificities

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Identification of conserved regulatory elements by comparative genome analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Genomic targets of the human c-Myc protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Database resources of the National Center for Biotechnology

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Additivity in protein-DNA interactions: how good an approximation is it?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

rVista for comparative sequence-based discovery of functional transcription factor binding sites

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

SAMIE: statistical algorithm for modeling interaction energies.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

GCN4 binds with high affinity to DNA sequences containing a single consensus half-site

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

DNA binding sites: representation and discovery

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Basic local alignment search tool

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

cAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Analysis of chromatin structure by in vivo formaldehyde cross-linking.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Searching for regulatory elements in human noncoding sequences.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Modeling within-motif dependence for transcription factor binding site predictions

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

NF-kappa B hyperactivation has differential effects on the APC function of nonobese diabetic mouse macrophages.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Probabilistic code for DNA recognition by proteins of the EGR family.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Genomic analysis of immediate/early response to shear stress in human coronary artery endothelial cells.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Elevated NF-kappaB activation in nonobese diabetic mouse dendritic cells results in enhanced APC function

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1142474

Dendritic cells from nonobese diabetic mice exhibit a defect in NF-kappa B regulation due to a hyperactive I kappa B kinase

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15930494

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.2952005

1 reference

20 September 2017

1 reference

20 September 2017

PubMed publication ID

15930494

1 reference