Normalized Affymetrix expression data are biased by G-quadruplex formation (Q34112136)

31 July 2017

title

Normalized Affymetrix expression data are biased by G-quadruplex formation (English)

1 reference

31 July 2017

Hugh P Shanahan

1

1 reference

31 July 2017

Farhat N Memon

series ordinal

2

1 reference

31 July 2017

Graham J G Upton

series ordinal

3

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31 July 2017

Andrew P Harrison

series ordinal

4

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31 July 2017

language of work or name

English

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publication date

22 December 2011

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31 July 2017

published in

Nucleic Acids Research

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31 July 2017

volume

40

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31 July 2017

issue

8

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31 July 2017

page(s)

3307-3315

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Creative Commons Attribution-NonCommercial 3.0 Unported

31 July 2017

copyright license

start time

8 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

GOBO: gene expression-based outcome for breast cancer online

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Algorithm-driven artifacts in median polish summarization of microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

On the causes of outliers in Affymetrix GeneChip data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

G-spots cause incorrect expression measurement in Affymetrix microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Analysis of probe level patterns in Affymetrix microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Normalization of microarray data: single-labeled and dual-labeled arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

NCBI GEO: mining tens of millions of expression profiles--database and tools update

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Quadruplex DNA: sequence, topology and structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Analysis of hybridization on the molecular barcode GeneChip microarray.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

A new summarization method for Affymetrix probe level data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Molecular characterization of bipolar disorder by comparing gene expression profiles of postmortem brains of major mental disorders

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

The Gene Ontology (GO) database and informatics resource

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Transformation and normalization of oligonucleotide microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Helix formation by guanylic acid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Summaries of Affymetrix GeneChip probe level data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Whole-genome expression analysis: challenges beyond clustering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Cluster analysis and display of genome-wide expression 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=3333884

Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Gene expression analysis of bipolar disorder reveals downregulation of the ubiquitin cycle and alterations in synaptic genes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Comparison of Affymetrix GeneChip expression measures.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Robust estimators for expression analysis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333884

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22199258

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR1230

1 reference

31 July 2017

1 reference

31 July 2017

1 reference