CoChat
Sign Up
Cited by 77

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations

Mabbott, Neil A., Kenneth Baillie, J., Hume, David A., Freeman, Tom C.·2010·Immunobiology
DOI 10.1016/j.imbio.2010.05.012
Open this paper in CoChat — free account

Abstract

In order to address fundamental questions associated with the relationships between mononuclear phagocytes and other myeloid and lymphoid cell populations, we have taken advantage of the growing body of expression data available in the public domain. We collated a large number of published expression studies on mouse haemopoietic cell lineages comprising 304 cell samples from 29 independent experiments performed on a single microarray platform (Affymetrix MOE430-2). The data were subjected to network-based cluster analysis using Biolayout Express(3D). Genes with related function clustered together in distinct regions of the graph reaffirming many known associations between gene expression and role in specific pathways and defining most major cell types of the immune system. Promoters of genes within individual clusters were distinguished by over-representation of regulatory motifs recognised by specific transcription factors. However, these data indicate that commonly used myeloid subpopulation markers, such as CD11c (Itgax), do not correlate with expression of other genes, and further bring into question their use in defining myeloid cell lineage, activation (M1 vs. M2) and antigen-presenting cell function. In particular, there were few mRNA markers that clearly distinguished classical dendritic cells (DC) from macrophages, other than low expression of genes required for phagocytic activity. Bone marrow-derived DC, grown in GM-CSF, were clearly identified as phagocytes and d…

Overview

Integrity signals

Registry

Crossref · 10.1016/j.imbio.2010.05.012

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Show all 6 references

Research works printed but not linked: 42

  1. Anderson, 2002, Projection of an immunological self shadow with the thymus by the aire protein, Science, 298, 1349, 10.1126/science.1075958 · DOI
  2. Aziz, 2006, Development of macrophages with altered actin organization in the absence of MafB, Molecular and Cellular Biology, 26, 6808, 10.1128/MCB.00245-06 · DOI
  3. Bar-On, 2010, Defining dendritic cells by conditional and constitutive cell ablation, Immunology Reviews, 234, 76, 10.1111/j.0105-2896.2009.00875.x · DOI
  4. Bar-On, 2010, Defining in vivo dendritic cell function using CD11c-DTR transgenic mice, Methods in Molecular Biology, 595, 429, 10.1007/978-1-60761-421-0_28 · DOI
  5. Bonifer, 2008, The transcriptional regulation of the colony-stimulating factor 1 receptor (csf1r) gene during hematopoiesis, Frontiers in Bioscience, 13, 549, 10.2741/2700 · DOI
  6. Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014 · DOI
  7. Chorro, 2009, Langerhans cell (LC) proliferation mediates neonatal development, homeostasis and inflammation-associated expansion of the epidermal LC network, Journal of Experimental Medicine, 206, 3089, 10.1084/jem.20091586 · DOI
  8. Crozat, 2010, Comparative genomics as a tool to reveal functional equivalences between human and mouse dendritic cell subsets, Immunology Reviews, 234, 177, 10.1111/j.0105-2896.2009.00868.x · DOI
  9. Fleetwood, 2009, GM-CSF- and M-CSF-dependent macrophage phenotypes display differential dependence on type I interferon signaling, Journal of Leukocyte Biology, 86, 411, 10.1189/jlb.1108702 · DOI · Paper page
  10. Fleetwood, 2007, Granulocyte-macrophage colony-stimulating factor (CSF) and macrophage CSF-dependent macrophage phenotypes display differences in cytokine profiles and transcription, Journal of Immunology, 178, 5245, 10.4049/jimmunol.178.8.5245 · DOI · Paper page
  11. Freeman, 2007, Construction, visualisation, and clustering of transcription networks from microarray expression data, PLoS Computational Biology, 3, 2032, 10.1371/journal.pcbi.0030206 · DOI · Paper page
  12. Frith, 2004, Detection of functional DNA motifs via statistical over-representation, Nucleic Acids Research, 32, 1372, 10.1093/nar/gkh299 · DOI
  13. Frith, 2003, Cluster-binding: finding dense clusters of motifs in DNA sequences, Nucleic Acids Research, 31, 3666, 10.1093/nar/gkg540 · DOI
  14. Geissmann, 2010, Development of monocytes, macrophages, and dendritic cells, Science, 327, 656, 10.1126/science.1178331 · DOI · Paper page
  15. Hargreaves, 2009, Control of inducible gene expression by signal-dependent transcription elongation, Cell, 138, 129, 10.1016/j.cell.2009.05.047 · DOI
  16. Hume, 2000, Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression, Blood, 96, 2323, 10.1182/blood.V96.7.2323 · DOI
  17. Hume, 2008, Differentiation and heterogeneity in the mononuclear phagocyte system, Mucosal Immunology, 1, 432, 10.1038/mi.2008.36 · DOI
  18. Hume, 2008, Macrophages as APC and the dendritic cell myth, Journal of Immunology, 181, 5829, 10.4049/jimmunol.181.9.5829 · DOI
  19. Hume, 2002, The mononuclear phagocyte system revisited, Journal of Leukocyte Biology, 72, 621, 10.1189/jlb.72.4.621 · DOI
  20. Hume, D.A., Summers, K.M., Raza, S., Baillie, J.K., Freeman, T.C., 2010. Functional clustering and lineage markers: insights into cellular differentiation and gene functions from large-scale microarray studies of purified primary cell populations. Genomics 95, 328–338 · DOI
  21. Ingersoll, 2010, Comparison of gene expression profiles between human and mouse monocyte subsets, Blood, 115, e10, 10.1182/blood-2009-07-235028 · DOI
  22. Irizarry, 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, 5, 249, 10.1093/biostatistics/4.2.249 · DOI · Paper page
  23. Jakubzick, 2008, Lymph-migrating, tissue-derived dendritic cells are minor constituents within steady-state lymph nodes, Journal of Experimental Medicine, 205, 2839, 10.1084/jem.20081430 · DOI
  24. Lattin, 2008, Expression analysis of G protein-coupled receptors in mouse macrophages, Immunome Research, 4, 5, 10.1186/1745-7580-4-5 · DOI
  25. Liu, 2010, Origin and development of dendritic cells, Immunology Reviews, 234, 45, 10.1111/j.0105-2896.2009.00879.x · DOI
  26. Martinez, 2009, Alternative activation of macrophages: an immunologic functional perspective, Annual Reviews of Immunology, 127, 451, 10.1146/annurev.immunol.021908.132532 · DOI · Paper page
  27. Medzhitov, 2009, Transcriptional control of the inflammatory response, Nature Reviews Immunology, 9, 692, 10.1038/nri2634 · DOI · Paper page
  28. Moriguchi, 2006, MafB is essential for renal development and F4/80 expression in macrophages, Molecular and Cellular Biology, 26, 5715, 10.1128/MCB.00001-06 · DOI
  29. Niehrs, 1999, Synexpression groups in eukaryotes, Nature, 402, 483, 10.1038/990025 · DOI
  30. Pavli, 1990, Isolation and characterization of antigen-presenting dendritic cells from the mouse intestinal lamina propria, Immunology, 70, 40
  31. Pletneva, 2009, IFN-producing killer dendritic cells are antigen-presenting cells endowed with T-cell cross-priming capacity, Cancer Research, 69, 6607, 10.1158/0008-5472.CAN-09-0508 · DOI
  32. Ravasi, 2002, Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes, Journal of Immunology, 168, 44, 10.4049/jimmunol.168.1.44 · DOI
  33. Ravasi, 2007, Systems biology of transcription control in macrophages, Bioessays, 29, 1215, 10.1002/bies.20683 · DOI
  34. Rehli, 1999, TFEC is a macrophage-restricted member of the microphthalmia-TFE subfamily of basic helix-loop-helix leucine zipper transcription factors, Journal of Immunology, 162, 1559, 10.4049/jimmunol.162.3.1559 · DOI · Paper page
  35. Sasmono, 2007, Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony-stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts and can transdifferentiate into macrophages in vitro in response to CSF-1, Journal of Leukocyte Biology, 82, 111, 10.1189/jlb.1206713 · DOI
  36. Su, 2002, Large-scale analysis of the human and mouse transcriptomes, Proceedings of the National Academy of Sciences USA, 99, 4465, 10.1073/pnas.012025199 · DOI · Paper page
  37. Tagoh, 2002, Transcription factor complex formation and chromatin fine structure alterations at the murine c-fms (CSF-1 receptor) locus during maturation of myeloid precursor cells, Genes and Development, 16, 1721, 10.1101/gad.222002 · DOI
  38. Tenen, 1997, Transcription factors, normal myeloid development, and leukemia, Blood, 90, 489, 10.1182/blood.V90.2.489 · DOI · Paper page
  39. Theocharidis, 2009, Network visualization and analysis of gene expression data using BioLayout Express(3D), Nature Protocols, 4, 1535, 10.1038/nprot.2009.177 · DOI
  40. Tsuchiya, 2009, Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages, PLoS ONE, 4, e4905, 10.1371/journal.pone.0004905 · DOI
  41. Wells, 2003, Genetic control of the innate immune response, BMC Immunology, 4, 5, 10.1186/1471-2172-4-5 · DOI
  42. Wu, 2009, BioGPS: an extensible and customized portal for querying and organizing gene annotation resources, Genome Biology, 10, R130, 10.1186/gb-2009-10-11-r130 · DOI

Cited by

Sorted by citations

See all 77

Metadata

Authors
Mabbott, N. A., Kenneth Baillie, J., Hume, D. A., & Freeman, T. C.
Venue
Immunobiology
Publisher
Elsevier BV
Published
2010-09
Volume
215
Issue
9-10
Pages
724-736
ISSN
0171-2985
DOI
10.1016/j.imbio.2010.05.012
Cited by
77
References
6
Language
en
Licence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. https://app.cochat.ai/papers/10.1016/j.imbio.2010.05.012
The paper
Mabbott, N. A., Kenneth Baillie, J., Hume, D. A., & Freeman, T. C. (2010). Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology. https://doi.org/10.1016/j.imbio.2010.05.012