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 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.
The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark.
Frederik Otzen
http://orcid.org/0000-0003-0636-8845
FO
Bagger
DTU Compute, Technical University of Denmark, Lyngby, Denmark.
Damir
D
Sasivarevic
DTU Compute, Technical University of Denmark, Lyngby, Denmark.
Sina Hadi
SH
Sohi
The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark.
Linea Gøricke
LG
Laursen
The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark.
Sachin
S
Pundhir
The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark.
Casper Kaae
CK
Sønderby
Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark DTU Compute, Technical University of Denmark, Lyngby, Denmark.
Ole
O
Winther
The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark nicolas.rapin@finsenlab.dk.
Nicolas
http://orcid.org/0000-0001-5208-8874
N
Rapin
The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark bo.porse@finsenlab.dk.
Bo T
BT
Porse
D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006410:Hematopoiesis / Q000235:genetics*; D006412:Hematopoietic Stem Cells / Q000378:metabolism; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D051379:Mice; D014158:Transcription, Genetic