A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis (Q34192877)

31 July 2017

title

A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis (English)

1 reference

31 July 2017

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Brian W Busser

1

1 reference

31 July 2017

Leila Taher

2

1 reference

31 July 2017

Yongsok Kim

3

1 reference

31 July 2017

Terese Tansey

4

1 reference

31 July 2017

Molly J Bloom

5

1 reference

31 July 2017

Ivan Ovcharenko

6

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31 July 2017

Alan M Michelson

7

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31 July 2017

publication date

8 March 2012

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31 July 2017

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31 July 2017

volume

8

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31 July 2017

issue

3

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31 July 2017

page(s)

e1002531

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Creative Commons CC0 License

31 July 2017

copyright license

start time

8 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

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Effects of sample size on robustness and prediction accuracy of a prognostic gene signature

5 July 2018

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ChIP-seq accurately predicts tissue-specific activity of enhancers

5 July 2018

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Teasing out T-box targets in early mesoderm

5 July 2018

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The genetics of vertebrate myogenesis

5 July 2018

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Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

5 July 2018

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Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

5 July 2018

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Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Muscle development: forming the head and trunk muscles.

5 July 2018

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Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

5 July 2018

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Global analysis of patterns of gene expression during Drosophila embryogenesis

5 July 2018

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Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

5 July 2018

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5 July 2018

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An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases

5 July 2018

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A core transcriptional network for early mesoderm development in Drosophila melanogaster

5 July 2018

1 reference

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Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

5 July 2018

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5 July 2018

1 reference

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VISTA Enhancer Browser--a database of tissue-specific human enhancers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Gene regulatory networks in the evolution and development of the heart

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Informative priors based on transcription factor structural class improve de novo motif discovery

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

A question of timing: emerging links between transcription and replication

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

c-Myb a stem-progenitor cell regulator in multiple tissue compartments.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

MyoD and the transcriptional control of myogenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Assisting Hox proteins in controlling body form: are there new lessons from flies (and mammals)?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Developmental gene amplification: insights into DNA replication and gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Highly conserved non-coding sequences are associated with vertebrate development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Coordinate enhancers share common organizational features in the Drosophila genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Control of pancreas and liver gene expression by HNF transcription factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Myb protein specificity: evidence of a context-specific transcription factor code.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Transcriptional integration of competence modulated by mutual repression generates cell-type specificity within the cardiogenic mesoderm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Regulation by homeoproteins: a comparison of deformed-responsive elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Evidence for stabilizing selection in a eukaryotic enhancer element.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The role of the NK-homeobox gene slouch (S59) in somatic muscle patterning

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Determination and development of the larval muscle pattern in Drosophila melanogaster

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The odor specificities of a subset of olfactory receptor neurons are governed by Acj6, a POU-domain transcription factor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Ultrabithorax function in butterfly wings and the evolution of insect wing patterns

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Transcriptional control of muscle development by myocyte enhancer factor-2 (MEF2) proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Combinatorial signaling codes for the progressive determination of cell fates in the Drosophila embryonic mesoderm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Muscle patterning and specification in Drosophila.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Regulation of segmentation and segmental identity by Drosophila homeoproteins: the role of DNA binding in functional activity and specificity.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The role of HOM-C genes in segmental transformations: reexamination of the Drosophila Sex combs reduced embryonic phenotype

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

twist: a myogenic switch in Drosophila.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The Drosophila gene pointed encodes two ETS-like proteins which are involved in the development of the midline glial cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The gene tinman is required for specification of the heart and visceral muscles in Drosophila

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Lethal of scute, a proneural gene, participates in the specification of muscle progenitors during Drosophila embryogenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Characterization and localization of the even-skipped protein of Drosophila

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Expression of a MyoD family member prefigures muscle pattern in Drosophila embryos

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Myogenesis: a view from Drosophila.

5 July 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Molecular integration of inductive and mesoderm-intrinsic inputs governs even-skipped enhancer activity in a subset of pericardial and dorsal muscle progenitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Collier transcription in a single Drosophila muscle lineage: the combinatorial control of muscle identity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Immunity regulatory DNAs share common organizational features in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Predicting gene expression from sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

The Dorsocross T-box genes are key components of the regulatory network controlling early cardiogenesis in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

The relative role of the T-domain and flanking sequences for developmental control and transcriptional regulation in protein chimeras of Drosophila OMB and ORG-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Apterous is a Drosophila LIM domain gene required for the development of a subset of embryonic muscles

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Reciprocal regulatory interactions between the Notch and Ras signaling pathways in the Drosophila embryonic mesoderm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Genetic programs activated by proneural proteins in the developing Drosophila PNS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Wingless signaling induces nautilus expression in the ventral mesoderm of the Drosophila embryo.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Tbx1 regulation of myogenic differentiation in the limb and cranial mesoderm

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Evolution of a transcriptional repression domain in an insect Hox protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Gene Selection for Cancer Classification using Support Vector Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1002531

Direct regulation of the muscle-identity gene apterous by a Hox protein in the somatic mesoderm.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

The role of Lbx1 in migration of muscle precursor cells.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Lbx1 is required for muscle precursor migration along a lateral pathway into the limb.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Regional specification of muscle progenitors in Drosophila: the role of the msh homeobox gene.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

wingless is required for the formation of a subset of muscle founder cells during Drosophila embryogenesis.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

Muscle pattern diversification in Drosophila is determined by the autonomous function of homeotic genes in the embryonic mesoderm

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297574

ladybird determines cell fate decisions during diversification of Drosophila somatic muscles

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22412381

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1002531

1 reference

31 July 2017

1 reference

31 July 2017

1 reference