Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences (Q28755362)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

title

Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences (English)

1 reference

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18 January 2020

1

1 reference

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18 January 2020

Aidan Budd

2

1 reference

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18 January 2020

Francois Spitz

3

1 reference

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18 January 2020

Joachim Wittbrodt

4

1 reference

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18 January 2020

author name string

Laurence Ettwiller

1

0 references

Aidan Budd

2

0 references

language of work or name

English

0 references

publication date

16 December 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

volume

9

1 reference

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18 January 2020

issue

12

1 reference

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18 January 2020

page(s)

R172

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

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

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

The evolutionary significance of cis-regulatory mutations

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Serum response factor binding sites differ in three human cell types

16 March 2017

1 reference

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The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

16 March 2017

1 reference

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Pfam: clans, web tools and services

16 March 2017

1 reference

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Core transcriptional regulatory circuitry in human embryonic stem cells

16 March 2017

1 reference

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Local regulatory variation in Saccharomyces cerevisiae

16 March 2017

1 reference

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Conservation and evolution of cis-regulatory systems in ascomycete fungi

16 March 2017

1 reference

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A common set of gene regulatory networks links metabolism and growth inhibition

16 March 2017

1 reference

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Control of pancreas and liver gene expression by HNF transcription factors

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1

16 March 2017

1 reference

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Human-mouse alignments with BLASTZ

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

16 March 2017

The Protein Data Bank

1 reference

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Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Identification of common molecular subsequences

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Improved tools for biological sequence comparison

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Transcriptional regulatory code of a eukaryotic genome

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Evolution of the mammalian transcription factor binding repertoire via transposable elements

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Divergence of transcription factor binding sites across related yeast species

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family

20 June 2018

1 reference

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Tissue-specific transcriptional regulation has diverged significantly between human and mouse

20 June 2018

1 reference

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Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Large-scale turnover of functional transcription factor binding sites in Drosophila

20 June 2018

1 reference

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Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

20 June 2018

1 reference

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Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues

20 June 2018

1 reference

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Perturbation of Ikaros isoform selection by MLV integration is a cooperative event in Notch(IC)-induced T cell leukemogenesis

20 June 2018

1 reference

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Turnover of binding sites for transcription factors involved in early Drosophila development.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Dynamic recruitment of NF-Y and histone acetyltransferases on cell-cycle promoters.

20 June 2018

1 reference

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Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells

20 June 2018

1 reference

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Emerging roles for E2F: Beyond the G1/S transition and DNA replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Comparative genomics: genome-wide analysis in metazoan eukaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Computational detection and location of transcription start sites in mammalian genomic DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Evidence for stabilizing selection in a eukaryotic enhancer element.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Role of E2F in cell cycle control and cancer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Purification of an MCM-containing complex as a component of the DNA replication licensing system.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Evolution of eukaryotic transcription circuits

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Differences between human and mouse embryonic stem cells

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646276

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19087242

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2008-9-12-R172

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

18 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19087242%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

1 reference