Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data. (Q30950123)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

title

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

1 reference

1 reference

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Nicole Cloonan

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Sean Grimmond

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Timothy J Bruxner

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

David K Miller

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

author name string

David L A Wood

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Katia Nones

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Anita Steptoe

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Ivon Harliwong

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Felicity Newell

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

language of work or name

English

0 references

publication date

12 May 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

page(s)

e0126911

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

8 March 2020

copyright license

start time

12 May 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Somatic point mutation calling in low cellularity tumors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Extensive variation in chromatin states across humans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Transcriptome and genome sequencing uncovers functional variation in humans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

A new strategy to reduce allelic bias in RNA-Seq readmapping

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Fast computation and applications of genome mappability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

AlleleSeq: analysis of allele-specific expression and binding in a network framework

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Regulation of X-chromosome inactivation by the X-inactivation centre.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Chromosome-wide analysis of parental allele-specific chromatin and DNA methylation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

The uniqueome: a mappability resource for short-tag sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

An imbalance of human complement regulatory proteins CFHR1, CFHR3 and factor H influences risk for age-related macular degeneration (AMD)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Variation in transcription factor binding among humans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Transcriptome genetics using second generation sequencing in a Caucasian population

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Fast and accurate long-read alignment with Burrows-Wheeler transform

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Mutations in the beta propeller WDR72 cause autosomal-recessive hypomaturation amelogenesis imperfecta

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

To localize or not to localize: mRNA fate is in 3'UTR ends

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

integrOmics: an R package to unravel relationships between two omics datasets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Common polymorphic transcript variation in human disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Stem cell transcriptome profiling via massive-scale mRNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Mapping the genetic architecture of gene expression in human liver

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genetics of gene expression and its effect on disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genomic imprinting effects on brain development and function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Heritability of alternative splicing in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genetic analysis of genome-wide variation in human gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Compound heterozygosity for non-sense and mis-sense mutations in desmoplakin underlies skin fragility/woolly hair syndrome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Effect of polymorphism in the human glutathione S-transferase A1 promoter on hepatic GSTA1 and GSTA2 expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Genomic imprinting: the emergence of an epigenetic paradigm.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0126911

Distinct patterns of gene-specific methylation in mammalian placentas: implications for placental evolution and function.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0126911

A regulatory single nucleotide polymorphism in the ubiquitin D gene associated with celiac disease.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0126911

Screening of pathogenic genes in Chinese patients with arrhythmogenic right ventricular cardiomyopathy

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4428808

Small changes in expression affect predisposition to tumorigenesis

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25965996

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0126911

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25965996%20AND%20SRC:MED&resulttype=core&format=json