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kuang-da/ft_cell_type_markers.json

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CellTypeAnnotation
Raw
ft_cell_type_markers.json
{
"Misc": {
"subtypes": {
"Extracellular Matrix": {
"markers": [
"Collagen IV"
],
"Anti_markers": [
"CD45",
"E-cadherin"
]
},
"Neuronal Cells": {
"markers": [
"CD146"
],
"Anti_markers": [
"SMA",
"Caveolin",
"ACTA2",
"VWF",
"CD44"
]
},
"Proliferating Cells": {
"markers": [
"Ki67"
]
}
}
},
"Mesenchymal Cells": {
"markers": [
"CD44"
],
"subtypes": {
"Fibroblasts": {
"markers": [
"Caveolin",
"CD34"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
},
"Anti_markers": [
"VWF",
"CD31",
"CD146"
]
},
"Smooth Muscle Cells": {
"markers": [
"Beta-actin",
"SMA",
"CD146",
"ACTA2"
],
"Anti_markers": [
"VWF",
"CD31"
]
}
},
"Anti_markers": [
"CD8",
"CD3e",
"CD4"
]
},
"Lymphoids": {
"subtypes": {
"B Cells": {
"markers": [
"CD20"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
},
"Anti_markers": [
"CD3e",
"E-cadherin",
"Pan-Cytokeratin"
]
},
"Natural-Killer (NK) Cells": {
"markers": [
"NKG2A"
],
"Anti_markers": [
"E-cadherin",
"Pan-Cytokeratin",
"CD3e"
]
},
"T Cells": {
"markers": [
"CD44",
"CD8",
"CD3e",
"CD4"
],
"subtypes": {
"Activated T Cells": {
"markers": [
"CD45RO"
],
"Anti_markers": [
"E-cadherin",
"Pan-Cytokeratin",
"CD20"
]
}
}
}
},
"Anti_markers": [
"E-cadherin",
"Pan-Cytokeratin"
]
},
"Stromal Fibroblasts": {
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
}
},
"Immune Cells": {
"markers": [
"Podoplanin",
"CD45"
],
"subtypes": {
"Myeloids": {
"markers": [
"CD14"
],
"subtypes": {
"Granulocytes": {
"markers": [
"CD68",
"CADPS"
],
"subtypes": {
"Neutrophils": {
"markers": [
"FUT4"
]
}
}
},
"Monocytes": {
"markers": [
"CD11b",
"CD68"
],
"subtypes": {
"Dendritic Cells": {
"markers": [
"CD11b"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Macrophages": {
"markers": [
"CD11b",
"CD68",
"HIF1A"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
}
},
"Anti_markers": [
"CADPS"
]
}
},
"Anti_markers": [
"E-cadherin",
"Pan-Cytokeratin",
"CD3e",
"CD20"
]
}
}
},
"DNA": {
"markers": [
"DAPI"
]
},
"Epithelium": {
"markers": [
"E-cadherin",
"Beta-actin",
"b-Catenin1",
"Pan-Cytokeratin"
],
"subtypes": {
"Ciliated Epithelium": {
"markers": [
"LGALS14",
"CDKN2A",
"FOXJ1",
"CADPS",
"DNALI1"
],
"Anti_markers": [
"CD68"
]
},
"Glandular Epithelium": {
"markers": [
"HLA-DR",
"EPCAM",
"CD105",
"PAX8",
"RUNX3",
"PGR",
"Keratin 8/18"
],
"subtypes": {
"Peg Cells": {
"markers": [
"CD44"
],
"Anti_markers": [
"CD8",
"CD3e",
"CD4"
]
}
},
"Anti_markers": [
"CD20",
"CD11b",
"CD68"
]
}
},
"Anti_markers": [
"CD45",
"CD31",
"Podoplanin"
]
},
"Endothelium": {
"markers": [
"Beta-actin"
],
"subtypes": {
"Lymphatic Endothelium": {
"markers": [
"Podoplanin"
],
"Anti_markers": [
"CD45",
"E-cadherin",
"Pan-Cytokeratin",
"CD31"
]
},
"Vascular Endothelium": {
"markers": [
"Caveolin",
"CD31",
"CD146",
"VWF"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
},
"Anti_markers": [
"SMA",
"ACTA2",
"Beta-actin",
"CD34"
]
}
},
"Anti_markers": [
"SMA",
"E-cadherin",
"b-Catenin1",
"Pan-Cytokeratin"
]
},
"_marker_map_metadata": {
"version": "v4_enhanced",
"description": "Enhanced marker map with additional anti-markers for NK, Lymphatic Endothelium, B Cells, and Myeloids to reduce false positives",
"changes_from_v3": [
"NK Cells: added E-cadherin, Pan-Cytokeratin, CD3e as anti-markers",
"Lymphatic Endothelium: added E-cadherin, Pan-Cytokeratin, CD31 as anti-markers",
"B Cells: added CD3e, E-cadherin, Pan-Cytokeratin as anti-markers",
"Myeloids: added E-cadherin, Pan-Cytokeratin, CD3e, CD20 as anti-markers",
"Activated T Cells: added E-cadherin, Pan-Cytokeratin, CD20 as anti-markers",
"Lymphoids parent: added E-cadherin, Pan-Cytokeratin as anti-markers",
"Epithelium: added CD45, CD31, Podoplanin as anti-markers",
"Extracellular Matrix: added CD45, E-cadherin as anti-markers"
],
"created_at": "2025-12-09"
}
}
Raw
ovary_11_13_cell_type_markers.json
{
"Mesenchymal Cells": {
"markers": [
"CD44"
],
"subtypes": {
"Fibroblasts": {
"markers": [
"CD34",
"Vimentin"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
},
"Anti_markers": [
"Caveolin",
"CD56",
"FOXL2"
]
},
"Smooth Muscle Cells": {
"markers": [
"SMA"
]
},
"Stromal Cells": {
"markers": [
"CD56",
"FOXL2",
"Vimentin"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
},
"Anti_markers": [
"Collagen IV",
"OGN",
"UCHL1",
"YAP1",
"CD34"
]
},
"Theca Cells": {
"markers": [
"GSTA1",
"STAR"
],
"subtypes": {
"Theca Externa Cells": {
"markers": [
"SMA"
]
}
}
}
},
"Anti_markers": [
"CD45RO"
]
},
"Misc": {
"subtypes": {
"Extracellular Matrix": {
"markers": [
"COL6A1",
"Collagen IV",
"OGN",
"Vimentin"
],
"Anti_markers": [
"FOXL2",
"CD34",
"CD56"
]
},
"Granulosa Cells": {
"markers": [
"FOXL2",
"YAP1"
],
"Anti_markers": [
"CD56"
]
},
"Neuronal Cells": {
"markers": [
"CD56",
"UCHL1"
],
"Anti_markers": [
"FOXL2"
]
},
"Oocytes": {
"markers": [
"UCHL1"
]
},
"Proliferating Cells": {
"markers": [
"Ki67"
]
}
}
},
"Immune Cells": {
"markers": [
"CD45",
"Podoplanin"
],
"subtypes": {
"Lymphoids": {
"subtypes": {
"B Cells": {
"markers": [
"CD20"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Cytotoxic T Cells": {
"markers": [
"CD8"
]
},
"T Cells": {
"markers": [
"CD3e"
],
"subtypes": {
"Activated T Cells": {
"markers": [
"CD44",
"CD45RO"
]
},
"CD4 T Cells": {
"markers": [
"CD4"
]
},
"CD8 T Cells": {
"markers": [
"CD8"
]
},
"Helper T Cells": {
"markers": [
"CD4"
]
}
}
}
}
},
"Myeloids": {
"markers": [
"CD14"
],
"subtypes": {
"Granulocytes": {
"markers": [
"CD68"
],
"Anti_markers": [
"CD11c"
]
},
"Monocytes": {
"markers": [
"CD11c",
"CD68"
],
"subtypes": {
"Dendritic Cells": {
"markers": [
"CD11c",
"CD68"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Macrophages": {
"markers": [
"CD11c",
"CD68"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
}
}
}
}
}
},
"Anti_markers": [
"DPP4"
]
},
"Epithelium": {
"markers": [
"b-Catenin1",
"Beta-actin",
"E-cadherin",
"Pan-Cytokeratin"
]
},
"Endothelium": {
"markers": [
"Caveolin",
"CD34"
],
"subtypes": {
"Lymphatic Endothelium": {
"markers": [
"DPP4",
"Podoplanin"
],
"Anti_markers": [
"CD45"
]
},
"Vascular Endothelium": {
"markers": [
"CD31",
"CLDN5"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
}
}
},
"Anti_markers": [
"Vimentin"
]
}
}
Raw
ovary_cell_type_markers.json
{
"Misc": {
"subtypes": {
"Extracellular Matrix": {
"markers": [
"Collagen IV",
"COL1A1",
"COL6A1",
"DCN",
"EMILIN",
"FN1",
"OGN",
"Vimentin"
]
},
"Granulosa Cells": {
"markers": [
"YAP1",
"PGR"
],
"subtypes": {
"Progesterone-Responsive Ovarian Cells": {
"markers": [
"PGR"
]
}
}
},
"Neuronal Cells": {
"markers": [
"UCHL1"
]
},
"Oocytes": {
"markers": [
"UCHL1"
]
},
"Proliferating Cells": {
"markers": [
"Ki67"
]
}
}
},
"Immune Cells": {
"markers": [
"CD45",
"Podoplanin"
],
"subtypes": {
"Lymphoids": {
"subtypes": {
"B Cells": {
"markers": [
"CD20",
"HLA-DR",
"HLA-A"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Cytotoxic T Cells": {
"markers": [
"CD8"
]
},
"T Cells": {
"markers": [
"CD44",
"CD3e",
"CD8",
"CD4",
"CD45RO"
],
"subtypes": {
"Activated T Cells": {
"markers": [
"CD44",
"CD45RO"
]
},
"CD4 T Cells": {
"markers": [
"CD4"
]
},
"CD8 T Cells": {
"markers": [
"CD8"
]
},
"Helper T Cells": {
"markers": [
"CD4"
]
}
}
}
}
},
"Myeloids": {
"markers": [
"CD14"
],
"subtypes": {
"Granulocytes": {
"markers": [
"CD68"
]
},
"Monocytes": {
"markers": [
"CD11c",
"CD68"
],
"subtypes": {
"Dendritic Cells": {
"markers": [
"HLA-DR",
"CD11c",
"CD68",
"HLA-A"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Macrophages": {
"markers": [
"HLA-DR",
"CD11c",
"CD68",
"HLA-A",
"IBAL"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
}
}
}
}
}
}
},
"Mesenchymal Cells": {
"markers": [
"CD44"
],
"subtypes": {
"Fibroblasts": {
"markers": [
"CD34",
"FN1",
"Vimentin"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Progesterone-Responsive Ovarian Cells": {
"markers": [
"PGR"
]
}
}
},
"Perivascular Cells": {
"markers": [
"PDGFRB"
],
"subtypes": {
"Progesterone-Responsive Ovarian Cells": {
"markers": [
"PGR"
]
}
}
},
"Smooth Muscle Cells": {
"markers": [
"SMA"
]
},
"Stromal Cells": {
"markers": [
"COL1A1",
"DCN",
"EMILIN",
"LUM",
"Vimentin",
"PDGFRB",
"HMGB1"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Avascular Cortical Cells": {
"markers": [
"HIF1A"
]
},
"Progesterone-Responsive Ovarian Cells": {
"markers": [
"PGR"
]
}
}
},
"Theca Cells": {
"markers": [
"GSTA1",
"STAR1",
"PGR"
],
"subtypes": {
"Progesterone-Responsive Ovarian Cells": {
"markers": [
"PGR"
]
},
"Theca Externa Cells": {
"markers": [
"SMA"
]
}
}
}
}
},
"Endothelium": {
"markers": [
"Caveolin",
"Podoplanin",
"CD34",
"CD31",
"VWF",
"CLDN5",
"DPP4"
],
"subtypes": {
"Lymphatic Endothelium": {
"markers": [
"Podoplanin",
"DPP4"
]
},
"Vascular Endothelium": {
"markers": [
"CD31",
"VWF",
"CLDN5"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
}
}
}
},
"Epithelium": {
"markers": [
"Beta-actin",
"E-cadherin",
"Pan-Cytokeratin",
"b-Catenin1",
"Keratin 8/18",
"EPCAM"
],
"subtypes": {
"Ovarian Surface Epithelium": {
"markers": [
"EPCAM"
]
}
}
}
}
Raw
uterus_cell_type_markers.json
{
"Misc": {
"subtypes": {
"Extracellular Matrix": {
"markers": [
"Collagen IV"
]
},
"Neuronal Cells": {
"markers": [
"CD146"
]
},
"Proliferating Cells": {
"markers": [
"Ki67"
]
},
"Stem Cells": {
"markers": [
"LGR5",
"Mushashi-1",
"CD15",
"LIFR",
"SUSD2",
"OCT4"
]
}
}
},
"Immune Cells": {
"markers": [
"Podoplanin",
"CD45RO"
],
"subtypes": {
"Lymphoids": {
"markers": [
"LIF",
"N-Cadherin"
],
"subtypes": {
"B Cells": {
"markers": [
"CD20"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Cytotoxic T Cells": {
"markers": [
"CD8"
]
},
"T Cells": {
"markers": [
"CD44",
"CD3e",
"CD8",
"CD4"
],
"subtypes": {
"Activated T Cells": {
"markers": [
"CD44"
]
},
"Helper T Cells": {
"markers": [
"CD4"
]
}
}
}
}
},
"Myeloids": {
"markers": [
"CD14"
],
"subtypes": {
"Granulocytes": {
"markers": [
"CD68"
],
"subtypes": {
"Neutrophils": {
"markers": [
"CD15"
]
}
}
},
"Monocytes": {
"markers": [
"CD11b",
"CD68"
],
"subtypes": {
"Dendritic Cells": {
"markers": [
"CD68"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
},
"Macrophages": {
"markers": [
"CD45",
"CD68"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Antigen-Presenting Cells (MHCII)": {
"markers": [
"HLA-DR"
]
}
}
}
}
}
}
}
}
},
"Mesenchymal Cells": {
"markers": [
"CD44"
],
"subtypes": {
"Fibroblasts": {
"markers": [
"CD34",
"PDGFR-B",
"CD140b"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
}
},
"Mesenchymal Stem Cells": {
"markers": [
"LIFR",
"SUSD2"
]
},
"Pericytes": {
"markers": [
"PDGFR-B",
"CD140b"
]
},
"Smooth Muscle Cells": {
"markers": [
"Beta-actin",
"SMA",
"CD146",
"PDGFR-B",
"CD140b"
]
},
"Stromal Fibroblasts": {
"markers": [
"PDGFR-B",
"CD140b"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
},
"Decidualization": {
"markers": [
"NOTCH1",
"SUSD2"
]
}
}
}
}
},
"Endothelium": {
"markers": [
"Caveolin",
"Podoplanin",
"CD34",
"CD31",
"Wnt7a"
],
"subtypes": {
"Luminal Endothelium": {
"markers": [
"Wnt7a"
]
},
"Lymphatic Endothelium": {
"markers": [
"Podoplanin"
]
},
"Vascular Endothelium": {
"markers": [
"CD31"
],
"subtypes": {
"Antigen-Presenting Cells (MHCI)": {
"markers": [
"HLA-A"
]
}
}
}
}
},
"Epithelium": {
"markers": [
"Beta-actin",
"E-cadherin",
"Pan-Cytokeratin",
"b-Catenin1",
"SMA",
"LIF",
"N-Cadherin",
"CD15",
"SOX9",
"DNALI1"
],
"subtypes": {
"Ciliated Epithelium": {
"markers": [
"SMA",
"DNALI1"
]
},
"Epithelial Stem Cells": {
"markers": [
"LGR5",
"Mushashi-1",
"CD15",
"LIFR"
]
},
"Glandular Epithelium": {
"markers": [
"b-Catenin1",
"LIF",
"CD15"
]
},
"Progenitor Epithelium": {
"markers": [
"N-Cadherin"
]
}
}
}
}
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