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BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis
Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet la...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702803/ https://www.ncbi.nlm.nih.gov/pubmed/26507857 http://dx.doi.org/10.1093/nar/gkv1101 |
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author | Bagger, Frederik Otzen Sasivarevic, Damir Sohi, Sina Hadi Laursen, Linea Gøricke Pundhir, Sachin Sønderby, Casper Kaae Winther, Ole Rapin, Nicolas Porse, Bo T. |
author_facet | Bagger, Frederik Otzen Sasivarevic, Damir Sohi, Sina Hadi Laursen, Linea Gøricke Pundhir, Sachin Sønderby, Casper Kaae Winther, Ole Rapin, Nicolas Porse, Bo T. |
author_sort | Bagger, Frederik Otzen |
collection | PubMed |
description | Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. |
format | Online Article Text |
id | pubmed-4702803 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-47028032016-01-07 BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis Bagger, Frederik Otzen Sasivarevic, Damir Sohi, Sina Hadi Laursen, Linea Gøricke Pundhir, Sachin Sønderby, Casper Kaae Winther, Ole Rapin, Nicolas Porse, Bo T. Nucleic Acids Res Database Issue Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. Oxford University Press 2016-01-04 2015-10-26 /pmc/articles/PMC4702803/ /pubmed/26507857 http://dx.doi.org/10.1093/nar/gkv1101 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Bagger, Frederik Otzen Sasivarevic, Damir Sohi, Sina Hadi Laursen, Linea Gøricke Pundhir, Sachin Sønderby, Casper Kaae Winther, Ole Rapin, Nicolas Porse, Bo T. BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title | BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title_full | BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title_fullStr | BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title_full_unstemmed | BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title_short | BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
title_sort | bloodspot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702803/ https://www.ncbi.nlm.nih.gov/pubmed/26507857 http://dx.doi.org/10.1093/nar/gkv1101 |
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