Application note: A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.

You can find here the supplement information describing in detail the workflow combining gensearchNGS with other tools used in the work published here:

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066
Published: 03 October 2019

News

Collaboration with PMCR

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Phenosystems is proud to announce our collaboration with PMCR GmbH based in Karlsruhe Germany. PMCR offers Peptide-based immunotherapies against cancer and infectious diseases – precise and effective, based on integrated individual multi-omics-analysis pipelines:

BITAP: targeted immune activation against cancer

BIVAP: T-cell immunisation against infectious diseases

BISS: Bioinformatics, integrated Multi-Omics Software solutions

These knowledge-platforms create a breakthrough of individualised precision medicine and will allow to greatly expand the services we can offer to our customers, offering solutions from sequence analysis to multi-omics knowledge and possible treatment options.

Please contact us to discuss your applications and need, we will work together towards a solution.

 

Clinvar introduces submission API

Clinvar has introduced an API to submit variant data. We will implement this shortly into our Gensearch and GensearchNGS products to replace the old FTP style semi-automatic submission tool.

In the meantime, please check whether your support and maintenance contract is up to date, if not, please contact your sales representative to extend your contract.

You can find out more about the API here.

Wuhan COVID19 upload module for German RKI

Germany has launched a national effort to fund sequencing of up to 10% of PCR samples taken from patients. A central database is being build at the Robert Koch Institut tasked to collect those sequences.

We have implemented a first version of an export module compatible with the requirements defined by the Robert Koch Institut.

You can download the latest version of our application note here.

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Hurry up! Our free licence offer for SARS-CoV2 labs ends April 30th 2021

We are offering a free licence for one year for our GensearchNGS software for any laboratory analysing SARS-CoV2 sequences to contribute to the fight against COVID19. Our offer will expire 30th April 2021, so please hurry to contact us to get your free one year licence!

You can download the latest version of our application note here.

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Application note: A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.

You can find here the supplement information describing in detail the workflow combining gensearchNGS with other tools used in the work published here:

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066
Published: 03 October 2019

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