(Q42239743)

19 October 2017

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b (English)

1 reference

19 October 2017

David M McGaughey

1

0 references

author name string

Ryan M Vinton

2

1 reference

19 October 2017

Jimmy Huynh

3

1 reference

19 October 2017

Amr Al-Saif

4

1 reference

19 October 2017

Michael A Beer

5

1 reference

19 October 2017

Andrew S McCallion

6

1 reference

19 October 2017

10 December 2007

1 reference

19 October 2017

1 reference

19 October 2017

18

1 reference

19 October 2017

252-260

1 reference

19 October 2017

2

1 reference

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

19 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Predicting tissue-specific enhancers in the human genome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Ancient noncoding elements conserved in the human genome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

In vivo enhancer analysis of human conserved non-coding sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Gene regulatory networks and the evolution of animal body plans

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Genomic regulatory networks and animal development

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Distribution and intensity of constraint in mammalian genomic sequence

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

PHOX2B genotype allows for prediction of tumor risk in congenital central hypoventilation syndrome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Highly conserved non-coding sequences are associated with vertebrate development

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Long-range control of gene expression: emerging mechanisms and disruption in disease

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Aligning multiple genomic sequences with the threaded blockset aligner

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Comparative genomic analysis as a tool for biological discovery

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Identification and characterization of multi-species conserved sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Transcription regulation and animal diversity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

The homeobox gene Phox2b is essential for the development of autonomic neural crest derivatives

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Expression and interactions of the two closely related homeobox genes Phox2a and Phox2b during neurogenesis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Stages of embryonic development of the zebrafish

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Phox2b function in the enteric nervous system is conserved in zebrafish and is sox10-dependent.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Into the heart of darkness: large-scale clustering of human non-coding DNA.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Predicting gene expression from sequence.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

PMX2B, a new candidate gene for Hirschsprung's disease.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

The apolipoprotein(a) gene is regulated by sex hormones and acute-phase inducers in YAC transgenic mice.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2203623

Conservation of RET regulatory function from human to zebrafish without sequence similarity

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18071029

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18071029

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.6929408

1 reference

19 October 2017

1 reference

19 October 2017

1 reference