EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data (Q33406619)

26 July 2017

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title

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data (English)

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26 July 2017

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16

Alfred Pühler

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Virginie Mittard-Runte

11

Virginie Mittard-Runte

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Tim Kahlke

Tim Kahlke

6

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Sebastian Jünemann

Sebastian Jünemann

5

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Alexander Goesmann

Alexander Goesmann

17

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Helge Küster

Helge Küster

8

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Andreas Tauch

14

Andreas Tauch

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26 July 2017

Michael Dondrup

1

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26 July 2017

Stefan P Albaum

2

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26 July 2017

Thasso Griebel

3

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26 July 2017

Kolja Henckel

4

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26 July 2017

Christiane K Kleindt

7

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26 July 2017

Burkhard Linke

9

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26 July 2017

Dominik Mertens

10

1 reference

26 July 2017

Virginie Mittard-Runte

11

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26 July 2017

Heiko Neuweger

12

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26 July 2017

Kai J Runte

13

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26 July 2017

Felix Tille

15

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26 July 2017

6 February 2009

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26 July 2017

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26 July 2017

10

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26 July 2017

50

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Creative Commons Attribution 2.0 Generic

26 July 2017

start time

6 February 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

describes a project that uses

SQL

1 reference

26 June 2022

https://europepmc.org/article/PMC/PMC2645365

based on heuristic

inferred from PubMed Central ID database lookup

affy

affy

1 reference

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

limma

LIMMA

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-10-50

0 references

cites work

The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

NCBI GEO: archive for high-throughput functional genomic data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Identification of Xanthomonas campestris pv. campestris galactose utilization genes from transcriptome data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Identification and expression regulation of symbiotically activated legume genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The MGED Ontology: a resource for semantics-based description of microarray experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Standardizing global gene expression analysis between laboratories and across platforms.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

MARS: microarray analysis, retrieval, and storage system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Bioconductor: open software development for computational biology and bioinformatics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

affy--analysis of Affymetrix GeneChip data at the probe level

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

EMMA: a platform for consistent storage and efficient analysis of microarray data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Normalization of cDNA microarray data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

GenDB--an open source genome annotation system for prokaryote genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

ArrayExpress--a public repository for microarray gene expression data at the EBI

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Design and implementation of microarray gene expression markup language (MAGE-ML)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Significance analysis of microarrays applied to the ionizing radiation response

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Using oligonucleotide probe arrays to access genetic diversity.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Characterization of a carbohydrate transporter from symbiotic glomeromycotan fungi.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Inferential literacy for experimental high-throughput biology

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645365

Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19200358

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19200358

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-10-50

1 reference

journals/bmcbi/DondrupAGHJKKKLMMNRTTPG09

26 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

26 July 2017

1 reference