An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors (Q36119908)

12 August 2017

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors (English)

1 reference

12 August 2017

2

Predrag Radivojac

1 reference

12 August 2017

Idit Kosti

1

1 reference

PMCID

3405991

12 August 2017

Yael Mandel-Gutfreund

series ordinal

3

1 reference

12 August 2017

26 July 2012

1 reference

PLOS Computational Biology

12 August 2017

1 reference

12 August 2017

8

1 reference

12 August 2017

7

1 reference

12 August 2017

e1002603

1 reference

Creative Commons Attribution 4.0 International

12 August 2017

start time

26 July 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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2 October 2017

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Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts

2 October 2017

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Integration of a splicing regulatory network within the meiotic gene expression program of Saccharomyces cerevisiae

2 October 2017

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Analysis and design of RNA sequencing experiments for identifying isoform regulation

2 October 2017

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Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans

2 October 2017

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Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls

2 October 2017

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Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets

2 October 2017

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Deciphering the splicing code

2 October 2017

1 reference

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

2 October 2017

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2 October 2017

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Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

2 October 2017

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Antagonistic factors control the unproductive splicing of SC35 terminal intron.

2 October 2017

1 reference

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Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

2 October 2017

1 reference

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Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity

2 October 2017

1 reference

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Large-scale proteomics analysis of the human kinome

2 October 2017

1 reference

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A computational approach for genome-wide mapping of splicing factor binding sites

2 October 2017

1 reference

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A census of human transcription factors: function, expression and evolution

2 October 2017

1 reference

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

2 October 2017

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Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

2 October 2017

1 reference

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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

2 October 2017

1 reference

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Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

2 October 2017

1 reference

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HITS-CLIP yields genome-wide insights into brain alternative RNA processing

2 October 2017

1 reference

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Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF

2 October 2017

1 reference

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High-quality binary protein interaction map of the yeast interactome network

2 October 2017

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Functional integration of transcriptional and RNA processing machineries

2 October 2017

1 reference

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Searching for splicing motifs.

2 October 2017

1 reference

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Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae.

2 October 2017

1 reference

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Coupling and coordination in gene expression processes: a systems biology view

2 October 2017

1 reference

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Regulation of alternative splicing by reversible protein phosphorylation

2 October 2017

1 reference

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Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli

2 October 2017

1 reference

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Global and local architecture of the mammalian microRNA-transcription factor regulatory network.

2 October 2017

1 reference

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

2 October 2017

1 reference

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Genetic reconstruction of a functional transcriptional regulatory network

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Eye development under the control of SRp55/B52-mediated alternative splicing of eyeless

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Intrinsic disorder in transcription factors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Length-dependent prediction of protein intrinsic disorder.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Cooperative actions of Tra2alpha with 9G8 and SRp30c in the RNA splicing of the gonadotropin-releasing hormone gene transcript

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Target RNA motif and target mRNAs of the Quaking STAR protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Nova autoregulation reveals dual functions in neuronal splicing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

A gene atlas of the mouse and human protein-encoding transcriptomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

The importance of intrinsic disorder for protein phosphorylation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

DAVID: Database for Annotation, Visualization, and Integrated Discovery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

The UCSC Genome Browser Database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

The protein kinase complement of the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Intrinsic disorder in cell-signaling and cancer-associated proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

An extensive network of coupling among gene expression machines

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Alternative splicing of intron 3 of the serine/arginine-rich protein 9G8 gene. Identification of flanking exonic splicing enhancers and involvement of 9G8 as a trans-acting factor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Regulated expression and RNA processing of transcripts from the Srp20 splicing factor gene during the cell cycle

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Developmental role of transcription factor isoforms generated by alternative splicing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

SFmap: a web server for motif analysis and prediction of splicing factor binding sites

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog?

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3405991

Exploring functional relationships between components of the gene expression machinery.

2 July 2018

1 reference

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Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Evolvability and hierarchy in rewired bacterial gene networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

An RNA map predicting Nova-dependent splicing regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Non-redundant functions of the protein isoforms arising from alternative splicing of the VEGF-A pre-mRNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Gene Expression: The Close Coupling of Transcription and Splicing

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002603

Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844237

12 December 2020

inferred from PubMed ID database lookup

Topological and causal structure of the yeast transcriptional regulatory network

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844237

12 December 2020

inferred from PubMed ID database lookup

Splicing factor Tra2-beta1 is specifically induced in breast cancer and regulates alternative splicing of the CD44 gene

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844237

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002603

1 reference

journals/ploscb/KostiRM12

12 August 2017

1 reference

DBLP Dataset 2021-01-02

release_affiy7b5kvhypbengd5bdcl4re

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/affiy7b5kvhypbengd5bdcl4re

24 November 2022

mapped directly with Wikidata item

PMCID

3405991

1 reference

12 August 2017

1 reference

PMCID

3405991