BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

By Frederik Otzen Bagger, Damir Sasivarevic, Sina Hadi Sohi, L. G. Laursen, S. Pundhir, Casper Kaae Sønderby, O. Winther, N. Rapin, B. Porse. Nucleic Acids Res., 2015

299 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Hematology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/61b8b8d1b7a7a208c6caaa6fe7ba60251bb949b7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. John Healy
2. Leland McInnes

In Hematology

1. John Healy
2. Leland McInnes

In Molecular Biology

1. Xiaoli Ru
2. T. Wen
3. Feng He
4. N. Rapin
5. Leland McInnes
6. John Healy

Citations in the corpus

• NRF2, a Transcription Factor for Stress Response and Beyond (2020, background): “In blood, monocytes, neutrophils, T cells, and B cells exhibit the high levels of NRF2 [119], suggesting”
• BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles (2018, background): “BloodSpot (1) is a database of haematopoietic cells in health and disease.”
• The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells (2017, unknown): “…diagram (1) enriched for m 6 A targets, (2) negatively enriched for transcripts upregulated after METTL3 depletion and (3) gene sets negatively enriched for transcripts with reduced translation efficiency in METTL3-depleted cells (For specific gene sets see Supplementary Tables 5, 6, 9 and 10).”