Reference:
Fetahu, I.S., Esser-Skala, W., Dnyansagar, R. et al. Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis. Nat Commun 14 3620 (2023). https://doi.org/10.1038/s41467-023-39210-0

GEPs with rescuing strategy

Program 1. Erythroblasts
Program 2. Lipid antigen activity
Program 3. B cells
Program 4. Immature dendritic cells
Program 5. T cells broad
Program 6. Neuroblastoma patient 21 specific
Program 7. Erythroblasts, late
Program 8. Plasma cells
Program 9. Immune cells
Program 10. Plasma cells patient 14 specific
Program 11. CD34 Pos HSCs
Program 12. Cancer program, ID genes in the top 50
Program 13. Gamma delta T cells
Program 14. Dendritic cells
Program 15. Cytokine-cytokine signaling
Program 16. Erythroid, megakaryocytes
Program 17. Unclear, possible activity program in few cells
Program 18. Plasmacytoid dendritic cells
Program 19. Complement expression activity
Program 20. Hematopoietic granulocyte-monocyte progenitors, curated markers are ranked 1, 2, 3
Program 21. Cancer cells, patients 19, 22 and others
Program 22. Mast cells, curated markers are ranked 4, 5, 6
Program 23. Cell cycle program
Program 24. B cells
Program 25. Monocytes
Program 26. Pro B-cells
Program 27. B cells
Program 28. Cell cycle program
Program 29. Unclear immune, possibly activity program
Program 30. T/NK cells
Program 31. Late erythroid
Program 32. Possibly activity program expressing T and NK cell-like features
Program 33. Monocytes/macrophages
Program 34. LYZ expressing inflammatory macrophages
Program 35. MHC Class II activity program
Program 36. Cancer program, ID expression high
Program 37. Cancer program, BMPR1B ranked 22
Program 38. Monocytes
Program 39. Monocytes/neutrophils
Program 40. NK cells
Program 41. Erythroblasts
Program 42. Interferon genes
Program 43. Cancer program
Program 44. CD8 T cells
Program 45. Pro B-cells
Program 46. Plasma cells
Program 47. Bone marrow platelets
Program 48. Bone marrow plasma cells
Program 49. Unclear, endothelial-like
Program 50. BMP2/4/5-expressiong bone marrow stromal cells
Program 51. Bone marrow plasma cells
Program 52. Non-inflammatory monocyte->macrophages

Reference:
Dong, Rui et al. Single-Cell Characterization of Malignant Phenotypes and Developmental Trajectories of Adrenal Neuroblastoma. Cancer Cell , Volume 38, Issue 5, 716 - 733.e6.

Dataset Specific GEPs

These GEPs don't appear in the network

Program 10. Neuroblastoma #2
Program 19. Neuroblastoma #5
Program 23. Pro-B Cells
Program 27. Schwannian Stromal Cell: NB

These GEPs appear in the network

Program 1. Endothelial
Program 2. Neuroblastoma #1
Program 3. Translation (Activity Program)
Program 4. Macrophage
Program 5. M2 Macrophage
Program 6. Cancer Associated Fibroblast: Inflammatory
Program 7. Cancer Associated Fibroblast: Myofibroblastic (POSTN+)
Program 8. Cell Cycle (G2-M)
Program 9. Adrenal Cortex Cells
Program 11. Neuroblastoma #3
Program 12. Schwannian Stromal Cell: GNB
Program 13. Erythroblasts
Program 14. Plasmacytoid Dendritic Cell
Program 15. Pre-B Cells
Program 16. Plasma Cells
Program 17. Neuroblastoma #4
Program 18. Endothelial: Lymphatic
Program 19. Neuroblastoma: Adrenergic II (pre-neuronal like)
Program 20. Cytotoxic T Cell
Program 21. Ganglioneuroblastoma Stromal
Program 22. Intermediate Monocyte
Program 24. Neuroblastoma: Adrenergic I (sympathoblast like)
Program 25. Cancer Associated Fibroblast: Intermediate [Myo:Inf]
Program 26. Naive B Cell
Program 28. Cell Cycle (G1/S)
Program 29. Myelocyte
Program 30. Cancer Associated Fibroblast: Intermediate [Inf:AP]
Program 31. Neuroblastoma: Adrenergic III
Program 32. Regulatory T Cell
Program 33. Neuroblastoma: MYCN
Program 34. Cancer Associated Fibroblast: Myofibroblastic (Contractile)
Program 35. Naive T Cell
Program 36. Neuroblastoma #5
Program 37. Neuroblastoma #6
Program 38. M1 Macrophage
Program 39. M-MDSC
Program 40. Cell Cycle (G1)
Program 41. IFN Response (Activity Program)

Reference:
Kildisiute, Gerda, et al. Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell. Sci. Adv. 7 , .6 (2021): eabd3311. DOI: 10.1126/sciadv.abd3311

Dataset Specific GEPs

These GEPs don't appear in the network

Program 12. GMP
Program 15. Megakaryocyte
Program 20. Keratin Expression
Program 23. Megakaryocyte-erythroid progenitors

These GEPs appear in the network

Program 1. Naive B Cell
Program 2. Inflammatory:cytokine signalling I
Program 3. Normal Adrenal Fibroblasts
Program 4. T Cell Activation
Program 5. Neuroblastoma: Adrenergic I (sympathoblast like)
Program 6. Hepatocyte-like Cell
Program 7. Endothelial: Vascular
Program 8. Monocyte/M-MDSC
Program 9. Adrenocortical Cells
Program 10. Erythroblasts
Program 11. Plasma Cells
Program 13. Cell Cycle (G2-M)
Program 14. Mature NKT Cells
Program 16. Mononuclear Phagocyte
Program 17. Undifferentiated lymphocyte
Program 18. Antigen Presentation
Program 19. Cancer Associated Fibroblast: Myofibroblastic (IGF1+)
Program 21. Mast Cells
Program 22. Neuroblastoma: MYCN
Program 24. M2 Macrophage
Program 25. Cancer Associated Fibroblast: Myofibroblastic (POSTN+)
Program 26. Pro-B Cells
Program 27. Endothelial: Lymphatic
Program 28. TNFa signalling via NFkB
Program 29. Endothelial
Program 30. Plasmacytoid Dendritic Cell
Program 31. Myelocyte
Program 32. Regulatory T Cell
Program 33. Monocyte: Inflammatory
Program 34. Natural killer cell (CD16+)
Program 35. Cancer Associated Fibroblast: Myofibroblastic (Contractile)
Program 36. Endothelial: Angiogenesis
Program 37. Naive T Cells
Program 38. CD8+ T Cells
Program 39. Neuroblastoma: Adrenergic II (pre-neuronal like)
Program 40. Fibroblast: Inflammatory
Program 41. Inflammatory: cytokine signalling II

Reference:
Jansky, S., Sharma, A.K., Körber, V. et al. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. Nat Genet 53 683–693 (2021). https://doi.org/10.1038/s41588-021-00806-1

Dataset Specific GEPs

These GEPs don't appear in the network

Program 1. Neuroblastoma #1
Program 7. Neuroblastoma #3
Program 13. Neuroblastoma #5
Program 14. Unknown NFkB
Program 16. Fetal Liver Hepatoblast-Like

These GEPs appear in the network

Program 2. Neuroblastoma #2
Program 3. Cancer Associated Fibroblast: Myofibroblastic (IGF1+)
Program 4. Macrophage
Program 5. Cancer Associated Fibroblast: Inflammatory
Program 6. Cancer Associated Fibroblast: Intermediate [Myo:Inf]
Program 8. Fibroblast/Hepatoblast-Like
Program 9. Endothelial
Program 10. Neuroblastoma: Adrenergic #1
Program 11. Neuroblastoma #4
Program 12. Neuroblastoma: Adrenergic #2
Program 15. Neuroblastoma #6
Program 17. Cancer Associated Fibroblast: Myofibroblastic (POSTN+)
Program 18. Neuroblastoma: MYCN

Reference:
Gerda Kildisiute et al. Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell. Sci. Adv. 7 , eabd3311(2021). DOI: 10.1126/sciadv.abd3311

Dataset Specific GEPs

These GEPs appear in the network

Program 1. Neuroblastoma: MYCN
Program 2. Myelocyte: Unknown
Program 3. Schwannain Stromal Cell
Program 4. M2 Macrophage
Program 5. Mast Cells
Program 6. Endothelial
Program 7. Cancer Associated Fibroblast: Intermediate [Myo:Inf] (IGF1+)
Program 8. Erythroblasts
Program 9. Neuroblastoma: Adrenergic I (sympathoblast like)
Program 10. Cytotoxic T Cell
Program 11. Cancer Associated Fibroblast: Myofibroblastic (POSTN+)
Program 12. Cancer Associated Fibroblast: Myofibroblastic
Program 13. Intermediate Monocyte
Program 14. Neuroblastoma: Adrenergic II (pre-neuronal like)
Program 15. Cancer Associated Fibroblast
Program 16. M-MDSC
Program 17. Cancer Associated Fibroblast: Myofibroblastic (Contractile)
Program 18. Cancer Associated Fibroblast: Inflammatory
Program 19. Regulatory T Cell

Reference:
Kameneva, P., Artemov, A.V., Kastriti, M.E. et al. Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nat Genet 53 , 694–706 (2021). https://doi.org/10.1038/s41588-021-00818-x
Verhoeven, Bronte Manouk et al. The immune cell atlas of human neuroblastoma. Cell Reports Medicine , Volume 3, Issue 6, 100657.

Dataset Specific GEPs

These GEPs don't appear in the network

Program 10. Neutrophil
Program 14. Fetal Kidney II (Podocytes)
Program 20. Hepatocyte-Like Cell II
Program 24. Fetal Kidney III
Program 29. Fetal Kidney IV

These GEPs appear in the network

Program 1. Plasma Cell
Program 2. Neuroblastoma: Adrenergic I
Program 3. Macrophage
Program 4. Fibroblast
Program 5. T Cell: Naive Helper T
Program 6. Fetal Kidney I
Program 7. Cancer Associated Fibroblast: Intermediate [Myo:Inf]
Program 8. Hepatocyte-Like Cell
Program 9. Endothelial I
Program 11. T Cell: Effector T Cell
Program 12. Adrenocortical Cells
Program 13. Monocyte
Program 15. Schwanninan Stromal Cell
Program 16. Macrophage II
Program 17. Erythroblasts
Program 18. T Cells: CD8+
Program 19. Cancer Associated Fibroblast: Myofibroblastic
Program 21. Stress Response
Program 22. Mast Cells
Program 23. M-MDSC
Program 25. Neuroblastoma: Adrenergic II
Program 26. Cell Cycle
Program 27. Plasmacytoid Dendritic Cell
Program 28. Cancer Associated Fibroblast: Inflammatory
Program 30. Natural Killer T Cell
Program 31. Endothelial
Program 32. Naive B Cell
Program 33. Neuroblastoma: Adrenergic III
Program 34. Neuroblastoma: Unknown
Program 35. Neuroblastoma: Adrenergic IV
Program 36. Endothelial
Program 37. Cancer Associated Fibroblast: Myofibroblastic (TAGLN+)
Program 38. Neuroblastoma: Adrenergic V
Program 39. Schwannian Stromal Cell II
Program 40. T Cell: Cytotoxic
Program 41. Inflammatory Macrophage
Program 42. Dendritic Cell
Program 43. T Cell: Regulatory