HaemAtlas protocols

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HaemAtlas specifications

Information


Unique identifier OMICS_15071
Name HaemAtlas
Interface Web user interface
Restrictions to use None
Input data Names of the genes.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Nicholas Watkins <>

Publication for HaemAtlas

HaemAtlas in pipeline

2017
PMCID: 5832629
PMID: 29239838
DOI: 10.1016/j.ebiom.2017.11.013

[…] set enrichment analysis (gsea (, ) version 1) was run with rank-ordered de gene lists for ca or ruxolitinib treatment. the signatures used for gsea included: tenedini_megakaryocyte_markers (msigdb), haematlas mk-specific gene set (extracted from arrayexpress accession e-tabm-633) (), and cfu-mk and mk specific gene set (extracted from geo accession gse24759) () gene lists were submitted to david […]


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HaemAtlas in publications

 (17)
PMCID: 5832629
PMID: 29239838
DOI: 10.1016/j.ebiom.2017.11.013

[…] set enrichment analysis (gsea (, ) version 1) was run with rank-ordered de gene lists for ca or ruxolitinib treatment. the signatures used for gsea included: tenedini_megakaryocyte_markers (msigdb), haematlas mk-specific gene set (extracted from arrayexpress accession e-tabm-633) (), and cfu-mk and mk specific gene set (extracted from geo accession gse24759) () gene lists were submitted to david […]

PMCID: 5607420
PMID: 28760933
DOI: 10.1128/IAI.00074-17

[…] profiles generated from whole blood of children in benin, published by idaghdour et al. (). we first defined a subset of erythroid cell-specific genes from the transcriptome based on the haematlas published by the bloodomics consortium () and from known blood groups. of 238 erythroid cell-specific/blood group transcripts from 61 healthy children included in the analysis, […]

PMCID: 5133527
PMID: 27980617
DOI: 10.1186/s12919-016-0011-3

[…] helper (cd4+) t-, and b-lymphocytes and monocytes in peripheral blood mononuclear cells from each individual was achieved by identifying gene expression signatures for different cell types from haematlas [] using 4879 probes that overlapped with the gaw19 data, and the quadratic programming algorithm of gong et al. [] as implemented in the r package cellmix []. examination of differences […]

PMCID: 5011717
PMID: 27596246
DOI: 10.1038/srep32976

[…] linear support vector regression, a machine learning approach highly robust with respect to noise, to deconvolve the mixture. we implemented the dsa algorithm in r and utilized cell markers from haematlas project. the marker list represented by array probes were downloaded from r package cellmix, and mapped to gene symbols. the cibersort r package and its associated leukocyte signature […]

PMCID: 4829662
PMID: 27052461
DOI: 10.1038/ncomms11208

[…] genes indicating appropriate downregulation of pluripotency features (). moreover, the gene set enrichment analysis against a panel of blood cells (cbmks versus other blood cells from haematlas; n=4 and 46, respectively) showed specific enrichment of mk-specific genes in the list of genes upregulated in fopmks further demonstrating the acquisition of a genuine mk phenotype […]


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HaemAtlas institution(s)
Department of Haematology, University of Cambridge, National Health Service Blood and Transplant, Cambridge, UK; Medical Research Council Biostatistics Unit, Institute of Public Health, University Forvie Site, Cambridge, UK; European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK; Wellcome Trust/Medical Research Council Building, Cambridge, UK; Division of Immunity and Infection, Medical Research Council Centre for Immune Regulation, University of Birmingham, Birmingham, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Haematology, Addenbrooke’s Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK; Department of Experimental Immunohaematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
HaemAtlas funding source(s)
This work was supported by the 6th Framework Programme of the European Union (LSHMCT-2004-503485), the National Institute for Health Research to National Health Service Blood and Transplant, the National Institute for Health Research Biomedical Research grant for Cambridge University Hospitals National Health Service Foundation Trust, and the Wellcome Trust.

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