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Protocols

integrOmics specifications

Information


Unique identifier OMICS_09001
Name integrOmics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.55
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kim-Anh Le Cao

Publication for integrOmics

integrOmics citations

 (65)
library_books

Exosomes from patients with septic shock convey miRNAs related to inflammation and cell cycle regulation: new signaling pathways in sepsis?

2018
PMCID: 5852953
PMID: 29540208
DOI: 10.1186/s13054-018-2003-3

[…] 65-A; Qiagen). Raw data were analyzed using ExpressionSuite v1.0.3 software (Life Technologies/Thermo Fisher Scientific), and all cycle threshold (Ct) values were evaluated using StatMiner version 5 (Integromics, Granada, Spain). Considering the cDNA preamplification step, Ct values greater than or equal to 32 for miRNAs and oxidative stress and greater than or equal to 35 for the immune study wer […]

library_books

From Genomics to Omics Landscapes of Parkinson's Disease: Revealing the Molecular Mechanisms

2018
PMCID: 5784788
PMID: 29356624
DOI: 10.1089/omi.2017.0181

[…] To take into account all the different omics layers, integromics (also termed integratomics or integrated omics) studies aim to find an overlap between results of individual omics. At least four integromics studies done on human samples have been recent […]

library_books

Long Noncoding RNA H19 Inhibits Cell Viability, Migration, and Invasion Via Downregulation of IRS 1 in Thyroid Cancer Cells

2017
PMCID: 5762077
PMID: 29332545
DOI: 10.1177/1533034617733904

[…] permix kit (Bio-Rad Laboratories, Hercules, CA, USA). The reaction was performed in triplicate for each sample at least 3 independent runs. The expression levels were analyzed by Real-Time StatMiner (Integromics, Madrid, Spain), and data were calculated by using 2−ΔΔCT method. […]

library_books

Alzheimer's brains show inter related changes in RNA and lipid metabolism

2017
PMCID: 5560656
PMID: 28630030
DOI: 10.1016/j.nbd.2017.06.008

[…] pression in RPKM with reference to the RefSeq gene structure; read counts with reference to each gene. Mapping and sequence/quality control metrics were generated both with the Lifetech suite and the Integromics SeqSolve analysis suite on all the samples. Read lengths were 75 nucleotide fragments, with a percentage of genome alignments over the whole sequence length over 80%. The minimal sequence […]

library_books

MicroRNA profile in neosquamous esophageal mucosa following ablation of Barrett’s esophagus

2017
PMCID: 5558114
PMID: 28852310
DOI: 10.3748/wjg.v23.i30.5508

[…] a Ct value of 40.To investigate whether any of the samples had low quality data we used the “detector profiling across samples” module in the RealTime PCR Statminer® software analysis program (v4.5, Integromics) to examine the correlations of Ct values between samples from the same epithelial tissue type across all of the amplified microRNAs. Samples that had multiple outliers were excluded from […]

call_split

Neuronal expressed microRNA targeted pseudogenes compete with coding genes in the human brain

2017
PMCID: 5611730
PMID: 28786976
DOI: 10.1038/tp.2017.163
call_split See protocol

[…] ion; gene expression in RPKM with reference to the RefSeq gene structure; and read counts with reference to each gene. Quality control metrics were generated both with the Lifetech suite and with the Integromics SeqSolve analysis suite on all the samples. TopHat 2.0.11 and Cufflinks 2.1.1 suite against GRCh38 genome sequence and associated ENSEMBL exon/transcript annotation in gtf format served to […]

Citations

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integrOmics institution(s)
Institute for Molecular Biosciences and ARC Centre of Excellence in Bioinformatics,The University of Queensland, Brisbane, Australia; Plateforme Biopuces, Genopôle Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées; Institut de Mathématiques de Toulouse, UMR 5219, Université de Toulouse et CNRS, France
integrOmics funding source(s)
Australian Research Council under the ARC Centres of Excellence program; ARC Centre of Excellence in Bioinformatics; Program on Food and Human Nutrition of the French National Research Agency, ANR PNRA 2006, project 2.23, plast-impact

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