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Annotare specifications

Information


Unique identifier OMICS_00741
Name Annotare
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Annotare

Annotare citations

 (17)
library_books

Comparison of the miRNA expression profiles in fresh frozen and formalin fixed paraffin embedded tonsillar tumors

2017
PMCID: 5482461
PMID: 28644855
DOI: 10.1371/journal.pone.0179645

[…] published studies, it is important to use the same type of clinical material and to test and select the best-performing normalization method for data analysis., supporting raw data were submitted to annotare. the data are publicly available from 7/6/2017 under accession e-mtab-5346., micrornas (mirnas) are small non coding rnas (~21 nucleotides) which play an important role […]

library_books

The role of the zinc finger protein ZC3H32 in bloodstream form Trypanosoma brucei

2017
PMCID: 5435347
PMID: 28545140
DOI: 10.1371/journal.pone.0177901

[…] zc3h32 might be implicated in basal mrna metabolism, with this role perhaps being taken over by another protein in procyclic forms., sequences from trypanosomes with reduced zc3h32 are available at annotare as e-mtab-4558; the rna immunoprecipitation is e-mtab-5612., organisms in the phylum euglenozoa rely on trans splicing to process mrnas from polycistronically transcribed precursors. […]

library_books

Intense light elicited upregulation of miR 21 facilitates glycolysis and cardioprotection through Per2 dependent mechanisms

2017
PMCID: 5407766
PMID: 28448534
DOI: 10.1371/journal.pone.0176243

[…] enhance mir-21 activity and subsequent carbohydrate metabolism in humans., all files are available through figshare at https://figshare.com/s/6b81501bf791f7004e66. array data are available through annotare at http://www.ebi.ac.uk/arrayexpress/experiments/e-mtab-5401., the rotation of the earth and associated light / dark cycles are responsible for entrainment of our circadian system, […]

library_books

The RNASeq er API—a gateway to systematically updated analysis of public RNA seq data

2017
PMCID: 5870697
PMID: 28369191
DOI: 10.1093/bioinformatics/btx143

[…] the analysis pipeline behind the rnaseq-er api offers an important service to researchers performing rna-seq experiments that choose to submit their data to arrayexpress via https://www.ebi.ac.uk/fg/annotare submission tool: the deposited studies are not only described by rich, ontology-annotated experimental metadata; the associated raw data is also analysed for free, and for qualifying […]

library_books

Reestablishment of p53/Arf and interferon β pathways mediated by a novel adenoviral vector potentiates antiviral response and immunogenic cell death

2017
PMCID: 5357668
PMID: 28386458
DOI: 10.1038/cddiscovery.2017.17

[…] distance and complete linkage. bootstrap was used to evaluate dendrogram’s consistency. enrichment analysis was performed in david database (ease score <0.05). data can be accessed through annotare repository (http://www.ebi.ac.uk/arrayexpress/experiments/e-mtab-5399)., the graphpad prism 5 software (la jolla, ca, usa) was used for statistical analyses. all comparisons were conducted […]

library_books

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

2017
PMCID: 5711377
PMID: 29110754
DOI: 10.7554/eLife.29132.031

[…] were performed by the university of michigan dna sequencing core using the illumina hi-seq 2500 platform. all sequences were deposited in the embl-ebi arrayexpress database (rrid:scr_004473) using annotare 2.0 and are cataloged under the accession number e-mtab-5801. transcriptional quantitation analysis was conducted using 64-bit debian linux stable version 7.10 ('wheezy’). pseudoalignment […]


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Annotare institution(s)
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA

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