(Q34478275)

2 August 2017

RNA-seq and microarray complement each other in transcriptome profiling. (English)

1 reference

2 August 2017

0 references

0 references

1 reference

Sunitha Kogenaru

1

1 reference

2 August 2017

Yan Qing

series ordinal

2

1 reference

2 August 2017

Yinping Guo

series ordinal

3

1 reference

2 August 2017

Nian Wang

series ordinal

4

1 reference

2 August 2017

language of work or name

English

0 references

publication date

15 November 2012

1 reference

2 August 2017

1 reference

2 August 2017

13

1 reference

2 August 2017

629

1 reference

describes a project that uses

2 August 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

object named as

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

6 July 2018

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Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

6 July 2018

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6 July 2018

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RNA-sequence analysis of human B-cells

6 July 2018

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Elucidation of the regulon and cis-acting regulatory element of HrpB, the AraC-type regulator of a plant pathogen-like type III secretion system in Burkholderia pseudomallei

6 July 2018

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The next-generation sequencing technology and application

6 July 2018

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The developmental transcriptome of Drosophila melanogaster

6 July 2018

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Quake: quality-aware detection and correction of sequencing errors

6 July 2018

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Effective--a database of predicted secreted bacterial proteins

6 July 2018

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Differential expression analysis for sequence count data

6 July 2018

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Uncovering the complexity of transcriptomes with RNA-Seq.

6 July 2018

1 reference

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Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria

6 July 2018

1 reference

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Most "dark matter" transcripts are associated with known genes

6 July 2018

1 reference

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

6 July 2018

1 reference

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Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

6 July 2018

1 reference

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RNA-Seq: a method for comprehensive transcriptome analysis

6 July 2018

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Gene expression analysis, proteomics, and network discovery.

6 July 2018

1 reference

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Regulation and secretion of Xanthomonas virulence factors

6 July 2018

1 reference

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A single-base resolution map of an archaeal transcriptome

6 July 2018

1 reference

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RNA-seq: from technology to biology

6 July 2018

1 reference

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The type III effectors of Xanthomonas

6 July 2018

1 reference

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Next generation sequencing of microbial transcriptomes: challenges and opportunities.

6 July 2018

1 reference

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Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing

6 July 2018

1 reference

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Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences.

6 July 2018

1 reference

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Estimating accuracy of RNA-Seq and microarrays with proteomics

6 July 2018

1 reference

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Transcript length bias in RNA-seq data confounds systems biology

6 July 2018

1 reference

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ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

6 July 2018

1 reference

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Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

6 July 2018

1 reference

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RNA-Seq: a revolutionary tool for transcriptomics

6 July 2018

1 reference

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Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

6 July 2018

1 reference

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cDNA cloning and function analysis of two novel erythroid differentiation related genes

6 July 2018

1 reference

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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

6 July 2018

1 reference

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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Stem cell transcriptome profiling via massive-scale mRNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The transcriptional landscape of the yeast genome defined by RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

How high is the level of technical noise in microarray data?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The type III secretion injectisome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Bioconductor: an open source framework for bioinformatics and computational biology

6 July 2018

1 reference

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Specific binding of the Xanthomonas campestris pv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoter boxes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Cloning of genes involved in pathogenicity of Xanthomonas campestris pv. campestris using the broad host range cosmid pLAFR1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Reliability and reproducibility issues in DNA microarray measurements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The transcriptional landscape of the mammalian genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Expression profiling of virulence and pathogenicity genes of Xanthomonas axonopodis pv. citri.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Type III secretion system effector proteins: double agents in bacterial disease and plant defense

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Cytoscape: a software environment for integrated models of biomolecular interaction networks

6 July 2018

1 reference

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cDNA microarray technology and its applications

6 July 2018

1 reference

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Evaluation of gene expression measurements from commercial microarray platforms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Characterization of the Xanthomonas axonopodis pv. glycines Hrp Pathogenicity Island

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

MARAN: normalizing micro-array data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

MatArray: a Matlab toolbox for microarray data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Comparison of the genomes of two Xanthomonas pathogens with differing host specificities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The KEGG databases at GenomeNet

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Molecular secrets of bacterial type III effector proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Unfolding of microarray data.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Analysis of variance for gene expression microarray data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

A concise guide to cDNA microarray analysis

6 July 2018

1 reference

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Cloning and molecular characterization of hrpX from Xanthomonas axonopodis pv. citri

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Gene ontology: tool for the unification of biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

DNA chips: state-of-the art.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The type III (Hrp) secretion pathway of plant pathogenic bacteria: trafficking harpins, Avr proteins, and death

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Use of a cDNA microarray to analyse gene expression patterns in human cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Sequence and expression analysis of the hrpB pathogenicity operon of Xanthomonas campestris pv. vesicatoria which encodes eight proteins with similarity to components of the Hrp, Ysc, Spa, and Fli secretion systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Conservation of secretion pathways for pathogenicity determinants of plant and animal bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

hrp genes of phytopathogenic bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Erwinia chrysanthemi and Pseudomonas syringae: plant pathogens trafficking in extracellular virulence proteins.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Multiplexed biochemical assays with biological chips

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Conservation of the hypersensitivity-pathogenicity regulatory gene hrpX of Xanthomonas campestris and X. oryzae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-13-629

Identification of novel type III secretion effectors in Xanthomonas oryzae pv. oryzae.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The beginning of the end for microarrays?

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Two Xanthomonas extracellular polygalacturonases, PghAxc and PghBxc, are regulated by type III secretion regulators HrpX and HrpG and are required for virulence.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

The role of hrp genes during plant-bacterial interactions

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

Microarrays: biotechnology's discovery platform for functional genomics.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534599

HrpG and HrpX play global roles in coordinating different virulence traits of Xanthomonas axonopodis pv. citri

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23153100

12 December 2020

inferred from PubMed ID database lookup

Microarrays: their origins and applications

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23153100

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2164-13-629

1 reference

release_56doel74bneyfhvkzw2magezku

2 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/56doel74bneyfhvkzw2magezku

24 November 2022

mapped directly with Wikidata item

PMCID

3534599

1 reference

2 August 2017

1 reference