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BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles
BloodSpot is a gene-centric database of mRNA expression of haematopoietic cells. The web-based interface to the database includes three concomitant levels of visualization for a gene query; foremost is the expression across hematopoietic cell types, second is analysis of survival of Acute Myeloid Le...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323996/ https://www.ncbi.nlm.nih.gov/pubmed/30395307 http://dx.doi.org/10.1093/nar/gky1076 |
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author | Bagger, Frederik Otzen Kinalis, Savvas Rapin, Nicolas |
author_facet | Bagger, Frederik Otzen Kinalis, Savvas Rapin, Nicolas |
author_sort | Bagger, Frederik Otzen |
collection | PubMed |
description | BloodSpot is a gene-centric database of mRNA expression of haematopoietic cells. The web-based interface to the database includes three concomitant levels of visualization for a gene query; foremost is the expression across hematopoietic cell types, second is analysis of survival of Acute Myeloid Leukaemia patients based on gene expression, and lastly, the expression visualized in an interactive developmental tree. With the introduction of single cell data we have now also included an unbiased dimensionality reduction method to show gene expression over the continuum of haematopoiesis. The webserver includes a few select analysis functionalities, like Student's t-test, identification of correlating genes and lookup of whole genetic signatures, with the aim of making generation and testing of hypotheses quick and intuitive. The visualizations have been updated to accommodate new datatypes and the database has been largely expanded with RNA-sequencing datasets, both purified in bulk and at single cell resolution, increasing the number of single samples more than 10 fold, while keeping simplicity in presentation. The database should be of interest for any researcher within leukaemia, haematopoiesis, cellular development, or stem cells. The database is freely available at www.bloodspot.eu |
format | Online Article Text |
id | pubmed-6323996 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-63239962019-01-10 BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles Bagger, Frederik Otzen Kinalis, Savvas Rapin, Nicolas Nucleic Acids Res Database Issue BloodSpot is a gene-centric database of mRNA expression of haematopoietic cells. The web-based interface to the database includes three concomitant levels of visualization for a gene query; foremost is the expression across hematopoietic cell types, second is analysis of survival of Acute Myeloid Leukaemia patients based on gene expression, and lastly, the expression visualized in an interactive developmental tree. With the introduction of single cell data we have now also included an unbiased dimensionality reduction method to show gene expression over the continuum of haematopoiesis. The webserver includes a few select analysis functionalities, like Student's t-test, identification of correlating genes and lookup of whole genetic signatures, with the aim of making generation and testing of hypotheses quick and intuitive. The visualizations have been updated to accommodate new datatypes and the database has been largely expanded with RNA-sequencing datasets, both purified in bulk and at single cell resolution, increasing the number of single samples more than 10 fold, while keeping simplicity in presentation. The database should be of interest for any researcher within leukaemia, haematopoiesis, cellular development, or stem cells. The database is freely available at www.bloodspot.eu Oxford University Press 2019-01-08 2018-11-05 /pmc/articles/PMC6323996/ /pubmed/30395307 http://dx.doi.org/10.1093/nar/gky1076 Text en © The Author(s) 2018. 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 Non-Commercial 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 Kinalis, Savvas Rapin, Nicolas BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title | BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title_full | BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title_fullStr | BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title_full_unstemmed | BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title_short | BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles |
title_sort | bloodspot: a database of healthy and malignant haematopoiesis updated with purified and single cell mrna sequencing profiles |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323996/ https://www.ncbi.nlm.nih.gov/pubmed/30395307 http://dx.doi.org/10.1093/nar/gky1076 |
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