Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets (Q34769866)

4 August 2017

title

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

1 reference

4 August 2017

1 reference

Chaim Linhart

1

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4 August 2017

Yonit Halperin

series ordinal

2

1 reference

4 August 2017

Ron Shamir

series ordinal

3

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4 August 2017

publication date

14 April 2008

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4 August 2017

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4 August 2017

volume

18

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4 August 2017

issue

7

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4 August 2017

page(s)

1180-1189

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Systematic functional characterization of cis-regulatory motifs in human core promoters

4 August 2017

cites work

1 reference

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7 July 2018

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7 July 2018

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

7 July 2018

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7 July 2018

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

7 July 2018

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

7 July 2018

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Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans

7 July 2018

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ChIP-chip comes of age for genome-wide functional analysis

7 July 2018

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The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation.

7 July 2018

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Cell-type-specific signatures of microRNAs on target mRNA expression

7 July 2018

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Core transcriptional regulatory circuitry in human embryonic stem cells

7 July 2018

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Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

7 July 2018

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An initial blueprint for myogenic differentiation

7 July 2018

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Assessing computational tools for the discovery of transcription factor binding sites

7 July 2018

1 reference

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E2Fs link the control of G1/S and G2/M transcription

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Transcriptional regulatory code of a eukaryotic genome

7 July 2018

1 reference

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Clustering of DNA sequences in human promoters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

CREME: Cis-Regulatory Module Explorer for the human genome

7 July 2018

1 reference

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Comprehensive analysis of the base composition around the transcription start site in Metazoa

7 July 2018

1 reference

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7 July 2018

An overview of Ensembl

1 reference

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

7 July 2018

1 reference

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The RNA polymerase II core promoter

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Computational analysis of core promoters in the Drosophila genome

7 July 2018

1 reference

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Discovery of novel transcription factor binding sites by statistical overrepresentation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Large clusters of co-expressed genes in the Drosophila genome.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Identification of genes periodically expressed in the human cell cycle and their expression in tumors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Chromatin profiling using targeted DNA adenine methyltransferase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Genomics, gene expression and DNA arrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

How does DNA methylation repress transcription?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

TRANSFAC: a database on transcription factors and their DNA binding sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Characterization of the human ADP-ribosylation factor 3 promoter. Transcriptional regulation of a TATA-less promoter

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493407

An algorithm for finding signals of unknown length in DNA sequences

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18411406

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Finding composite regulatory patterns in DNA sequences

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18411406

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.076117.108

1 reference

4 August 2017

1 reference

4 August 2017

1 reference