Dataset Information

VANTED v2: a framework for systems biology applications.

ABSTRACT:

Background

Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets.

Results

Here we present VANTED (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives. We describe the system as well as an exemplary workflow.

Conclusions

VANTED is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org.

SUBMITTER: Rohn H

PROVIDER: S-EPMC3610154 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature

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Publications

VANTED v2: a framework for systems biology applications.

Rohn Hendrik H Junker Astrid A Hartmann Anja A Grafahrend-Belau Eva E Treutler Hendrik H Klapperstück Matthias M Czauderna Tobias T Klukas Christian C Schreiber Falk F

BMC systems biology 20121110

<h4>Background</h4>Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets.<h4>Results</h4>Here we present VANTED (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconst ...[more]

PMID: 23140568

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Project description:Hematopoietic stem cells (HSCs) are at the basis of the hematopoietic hierarchy. Their ability to self-renew and differentiate is strictly controlled by molecular signals produced by their surrounding micorenvironments composed of stromal cells. HSCs first emerge in the AGM (Aorta Gonads Mesonephros) region, amplify in the fetal liver (FL) and are maintained in the adult bone marrow (BM). To further characterize the molecular program of the HSC niches, we have compared the global transcriptome of HSC-supportive and non-supportive stromal clones established from the AGM, FL and BM. Hematopoietic stem cells (HSCs) are at the basis of the hematopoietic hierarchy. Their ability to self-renew and differentiate is strictly controlled by molecular signals produced by their surrounding micorenvironments composed of stromal cells. HSCs first emerge in the AGM (Aorta Gonads Mesonephros) region, amplify in the fetal liver (FL) and are maintained in the adult bone marrow (BM). To further characterize the molecular program of the HSC niches, we have compared the global transcriptome of HSC-supportive line from Fetal Calvaria (OP9) and non-supportive stromal clones from fetal liver (BFC). Hematopoietic stem cells (HSCs) are at the basis of the hematopoietic hierarchy. Their ability to self-renew and differentiate is strictly controlled by molecular signals produced by their surrounding micorenvironments composed of stromal cells. HSCs first emerge in the AGM (Aorta Gonads Mesonephros) region, amplify in the fetal liver (FL) and are maintained in the adult bone marrow (BM). To further characterize the molecular program of the HSC niches, we have compared the global transcriptome of HSC-supportive and non-supportive stromal clones established from fetal liver. We took advantage of stromal clones established from the AGM, FL and BM and tested for their ability to support or not HSCs ex vivo. RNA were extracted from confluent stromal cultures or sorted cells and used for hybridization of Affymetrix (mouse gene 1.0 ST) microarrays.

Dataset Information

VANTED v2: a framework for systems biology applications.

Background

Results

Conclusions

Publications

VANTED v2: a framework for systems biology applications.

Similar Datasets

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