diff --git a/client/src/components/geneExpression/geneSet.js b/client/src/components/geneExpression/geneSet.js new file mode 100644 index 00000000..357cdd92 --- /dev/null +++ b/client/src/components/geneExpression/geneSet.js @@ -0,0 +1,33 @@ +// jshint esversion: 6 +/* rc slider https://www.npmjs.com/package/rc-slider */ + +import React from "react"; +import _ from "lodash"; +import { connect } from "react-redux"; +import HistogramBrush from "../brushableHistogram"; +import * as globals from "../../globals"; +import actions from "../../actions"; + +@connect(state => { + return {}; +}) +class GeneSet extends React.Component { + constructor(props) { + super(props); + this.state = {}; + } + + render() { + const { setName, setGenes } = this.props; + return ( +
+ {setName} + {_.map(setGenes, gene => { + return

{gene}

; + })} +
+ ); + } +} + +export default GeneSet; diff --git a/client/src/components/geneExpression/index.js b/client/src/components/geneExpression/index.js index 2af9455a..e647c01b 100644 --- a/client/src/components/geneExpression/index.js +++ b/client/src/components/geneExpression/index.js @@ -4,8 +4,8 @@ import React from "react"; import _ from "lodash"; import fuzzysort from "fuzzysort"; - import { connect } from "react-redux"; +import { Suggest } from "@blueprintjs/select"; import { MenuItem, Button, @@ -13,7 +13,6 @@ import { InputGroup, ControlGroup } from "@blueprintjs/core"; -import { Suggest } from "@blueprintjs/select"; import HistogramBrush from "../brushableHistogram"; import * as globals from "../../globals"; import actions from "../../actions"; @@ -21,8 +20,10 @@ import { postUserErrorToast, keepAroundErrorToast } from "../framework/toasters"; +import GeneSet from "./geneSet"; import { memoize } from "../../util/dataframe/util"; +import testGeneSets from "./test_data"; const renderGene = (fuzzySortResult, { handleClick, modifiers }) => { if (!modifiers.matchesPredicate) { @@ -142,6 +143,18 @@ class GeneExpression extends React.Component { return undefined; }; + renderTestGeneSets = () => { + const sets = []; + + _.forEach(testGeneSets, (setGenes, setName) => { + sets.push( + + ); + }); + + return sets; + }; + placeholderGeneNames() { /* return a string containing gene name suggestions for use as a user hint. @@ -362,6 +375,7 @@ class GeneExpression extends React.Component { }) : null} +
{this.renderTestGeneSets()}
); } diff --git a/client/src/components/geneExpression/test_data.js b/client/src/components/geneExpression/test_data.js new file mode 100644 index 00000000..eb1fe7a3 --- /dev/null +++ b/client/src/components/geneExpression/test_data.js @@ -0,0 +1,3220 @@ +import _ from "lodash"; + +const _testGeneSets = [ + { + "BLADDER.EPITHELIAL_UROTHELIAL.UMBRELLA_CELL": "EPCAM", + "BLADDER.EPITHELIAL_UROTHELIAL.BASAL_CELL": "EPCAM", + "BLADDER.MESENCHYMAL.NA": "DCN", + "FAT.NA.MESENCHYMAL_PROGENITORS": "PDGFRA", + "FAT.IMMUNE_CELLS.B_CELLS": "CD19", + "FAT.IMMUNE_CELLS.T_CELLS": "CD3G", + "FAT.IMMUNE_CELLS.NK_CELLS": "IRF8", + "FAT.IMMUNE_CELLS.MYELOID": "ITGAM", + "FAT.NA.ENDOTHELIAL_CELLS": "PECAM1", + "HEART_AND_AORTA.VASCULAR_ENDOTHELIAL.NA": "FABP4", + "HEART_AND_AORTA.FIBROBLASTS.NA": "DDR2", + "HEART_AND_AORTA.ATRIAL_CARDIOMYOCYTES.NA": "NPPA", + "HEART_AND_AORTA.ENDOCARDIAL.NA": "NPR3", + "HEART_AND_AORTA.IMMUNE.NA": "C1QA", + "HEART_AND_AORTA.MYOFIBROBLASTS.NA": "TCF21", + "HEART_AND_AORTA.SMOOTH_MUSCLE.NA": "MYH11", + "HEART_AND_AORTA.CARDIOMYOCYTES.NA": "TNNI3", + "HEART_AND_AORTA.AORTIC_ENDOTHELIAL.NA": "EHD3", + "HEART_AND_AORTA.ENDOTHELIAL.NA": "CDH5", + "HEART_AND_AORTA.ANTIGEN_PRESENTING.NA": "PTPRC", + "HEART_AND_AORTA.MACROPHAGES.NA": "SELPLG", + "KIDNEY.FENESTRATED_ENDOTHELIAL_CELLS.NA": "PLVAP", + "KIDNEY.MESANGIAL_CELLS.NA": "DES", + "KIDNEY.PODOCYTES.NA": "PODXL", + "KIDNEY.TUBULE.PROXIMAL_BRUSH_BORDER_CELLS": "WIL1", + "KIDNEY.TUBULE.DISTAL_COLLECTING_DUCT_PRINCIPAL_CELLS": "KCNE1", + "PANCREAS.EXOCRINE.ACINAR_CELLS": "AMY2B", + "PANCREAS.EXOCRINE.DUCTAL_CELLS": "KRT19", + "PANCREAS.ENDOCRINE.BETA": "INS1", + "PANCREAS.ENDOCRINE.ALPHA": "GCG", + "PANCREAS.ENDOCRINE.DELTA": "SST", + "PANCREAS.ENDOCRINE.PP": "PPY", + "PANCREAS.NA.ENDOTHELIAL": "KDR", + "PANCREAS.NA.IMMUNE": "PTPRC", + "PANCREAS.NA.STELLATE_CELLS": "PDGFRA", + "SPLEEN.IMMUNE.B_CELLS": "CD79A", + "SPLEEN.IMMUNE.T_CELLS": "CD4", + "TRACHEA.EPITHELIUM.CILIATED": "EPCAM", + "TRACHEA.EPITHELIUM.SECRETORY": "EPCAM", + "TRACHEA.EPITHELIUM.NEUROENDOCRINE": "EPCAM", + "TRACHEA.EPITHELIUM.BASAL": "EPCAM", + "TRACHEA.NA.MESENCHYMAL": "PDGFRB", + "TRACHEA.NA.IMMUNE": "PTPRC", + "TRACHEA.NA.ENDOTHELIAL": "PECAM1", + "TONGUE.EPITHELIUM.PROLIFERATIVE_BASAL": "TOP2A", + "TONGUE.EPITHELIUM.BASAL_KERATINOCYTES": "KRT10", + "TONGUE.EPITHELIUM.SUPRABASAL_BASAL_KERATINOCYTES": "KRT14", + "TONGUE.EPITHELIUM.FILIFORM_ASSOCIATED_KERATINOCYTES": "KRT84", + "TONGUE.EPITHELIUM.TASTE_RECEPTOR_CELLS": "KRT8", + "MARROW.WHOLE_MARROW.T_CELLS": "AHNAK", + "MARROW.WHOLE_MARROW.NK_CELLS": "KLRB1A", + "MARROW.WHOLE_MARROW.NKT_CELLS": "AHNAK", + "MARROW.WHOLE_MARROW.IMMATURE_T_CELLS": "CD3E", + "MARROW.WHOLE_MARROW.IMMATURE_NK": "KLRB1A", + "MARROW.WHOLE_MARROW.IMMATURE_NKT": "CD3E", + "MARROW.WHOLE_MARROW.PRE_NK": "MKI67", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.PRO_B": "DNTT", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.LATE_PRO_B": "PAX5", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.IMMATURE_B": "CHCHD10", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.MATURE_NAIVE_B": "CD79A", + "MARROW.TER119_B220_FACTION.LATE_PRO_B": "VPREB1", + "MARROW.TER119_B220_FACTION.INTERMEDIATE_PRE_B": "PAX5", + "MARROW.TER119_B220_FACTION.IMMATURE_B": "PAX5", + "MARROW.TER119_B220_FACTION.MATURE_NAIVE_B": "PAX5", + "MARROW.UNFRACTIONED_MARROW.HEMATOPOIETIC_PRECURSOR_CELLS": "KIT", + "MARROW.UNFRACTIONED_MARROW.PROERYTHOBLASTS": "TFRC", + "MARROW.UNFRACTIONED_MARROW.ERYTHOBLASTS": "BPGM", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_GRANULOPOIETIC_CELLS": "LTF", + "MARROW.UNFRACTIONED_MARROW.GRANULOCYTES": "LTF", + "MARROW.UNFRACTIONED_MARROW.BASOPHILS": "CCL3", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_PROMONOCYTE": "AHNAK", + "MARROW.UNFRACTIONED_MARROW.MATURE_MONOCYTES": "AHNAK", + "MARROW.UNFRACTIONED_MARROW.BM_MACROPHAGES": "AHNAK", + "MARROW.SUBFRACTIONATION.HPC_CLUSTERS": "KIT", + "MARROW.SUBFRACTIONATION.QUIESCENT_HSC_ENRICHED_FRACTION": "CD48", + "MARROW.SUBFRACTIONATION.MPPS": "STMN1", + "MARROW.SUBFRACTIONATION.MEGAKARYOCYTE_ERYTHROCYTE_PROGENITOR": "TGM2", + "MARROW.SUBFRACTIONATION.COMMON_LYMPHOCYTE_PROGENITOR_LINEAGE": "DNTT", + "MARROW.MYELOID_CELLS.GRANULOCYTE_MONOCYTE_PROGENITORS": "FLT3", + "MARROW.MYELOID_CELLS.MATURE_MONOCYTES": "CD68", + "MARROW.MYELOID_CELLS.MACROPHAGES": "CD68", + "MARROW.MYELOID_CELLS.GRANULOCYTE_1": "LTF", + "MARROW.MYELOID_CELLS.GRANULOCYTE_2_BASOPHILS": "CCL3", + "LUNG.EPITHELIAL.MULTICILIATED": "FOXJ1", + "LUNG.EPITHELIAL.ALVEOLAR_TYPE_2": "SFTPA1", + "LUNG.ENDOTHELIAL.NA": "PECAM1", + "LUNG.STROMAL.NA": "COL1A1", + "LUNG.IMMUNE.ALVEOLAR_MACROPHAGES": "MARCO", + "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGES": "CSF1R", + "LUNG.IMMUNE.DENDRITIC_CELLS": "ITGAX", + "LUNG.IMMUNE.INVADING_MONOCYTES": "ITGAM", + "LUNG.IMMUNE.NON_CANONICAL_1": "ITGAM", + "LUNG.IMMUNE.NON_CANONICAL_2": "ITGAM", + "LUNG.STROMA.ADVENTITIAL_FIBROBLAST": "SERPINF1", + "LUNG.STROMA.SCA1_ADVENTITIAL_FIBROBLAST": "SCARA5", + "LUNG.STROMA.ALVEOLAR_FIBROBLAST": "SLC7A10", + "LUNG.STROMA.MESOTHELIAL_CELL": "MSLN", + "LUNG.STROMA.MYOFIBROBLAST": "HHIP", + "LUNG.STROMA.PERICYTE": "TRPC6", + "LUNG.STROMA.SMOOTH_MUSCLE_CELL": "ACTA2", + "LUNG.STROMA.CHONDROCYTE": "SOX9", + "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_1_CELL": "CLIC5", + "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_2_CELL": "SFTPA1", + "LUNG.EPITHELIUM.CILIATED_CELL": "FOXJ1", + "LUNG.EPITHELIUM.NEUROENDOCRINE_CELL": "CALCA", + "LUNG.EPITHELIUM.BASAL_CELL": "KRT5", + "LUNG.EPITHELIUM.CLUB_CELL": "SCGB1A1", + "LUNG.EPITHELIUM.GOBLET_CELL": "MUC5B", + "LUNG.IMMUNE.ALVEOLAR_MACROPHAGE": "MARCO", + "LUNG.IMMUNE.B_CELL": "CD79A", + "LUNG.IMMUNE.BASOPHIL": "FCER1A", + "LUNG.IMMUNE.CLASSICAL_MONOCYTE": "CD14", + "LUNG.IMMUNE.DENDRITIC_CELL": "FLT3", + "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGE": "C1QA", + "LUNG.IMMUNE.NATURAL_KILLER_CELL": "NKG7", + "LUNG.IMMUNE.NEUTROPHIL": "RETNLG", + "LUNG.IMMUNE.NONCLASSICAL_MONOCYTE": "EMR4", + "LUNG.IMMUNE.CD4_T_CELL": "CD4", + "LUNG.IMMUNE.CD8_T_CELL": "CD8B1", + "LUNG.IMMUNE.INTERMEDIATE_MONOCYTE": "PLAC8", + "LUNG.IMMUNE.NATURAL_KILLER_T_CELL": "CXCR6", + "LUNG.IMMUNE.PLASMACYTOID_DENDRITIC_CELL": "SIGLECH", + "LUNG.IMMUNE.PROLIFERATING_ALVEOLAR_MACROPHAGE": "MKI67", + "LUNG.IMMUNE.PROLIFERATING_NK_T_CELL": "CXCR6", + "LUNG.ENDOTHELIUM.ARTERY_CELL": "DKK2", + "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_1_CELL": "PLVAP", + "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_2_CELL": "EDNRB", + "LUNG.ENDOTHELIUM.LYMPHATIC_CELL": "PROX1", + "LUNG.ENDOTHELIUM.VEIN_CELL": "SLC6A2", + "LUNG.NEURONAL_GLIA.GLIAL_CELL": "ARHGAP42", + "LIVER.NA.ENDOTHELIUM": "PECAM1", + "LIVER.NA.STELLATE_CELLS": "DCN", + "LIVER.HEPATOCYTES.PERICENTRAL_PERIPORTAL_MIDLOBULAR": "ALB", + "LIVER.IMMUNE.KUPFFER_MACROPHAGE": "EMR1", + "LIVER.IMMUNE.NK_NKT_CELLS": "ZAP70", + "LIVER.IMMUNE.CIRCULATING_B_CELLS": "CD79A", + "LIVER.IMMUNE.MACROPHAGES_MONOCYTES": "MRC1", + "LIVER.IMMUNE.T_CELLS": "CD3E", + "LIVER.CHOLANGIOCYTES_BILE_DUCT_EPITHELIAL_CELLS.NA": "EPCAM", + "LIVER.IMMUNE.NEUTROPHILS": "CSF3R", + "LIVER.IMMUNE.PLASMACYTOID_DENDRITIC": "SIGLECH", + "LIVER.ERYTHROCYTES.NA": "BPGM", + "LARGE_INTESTINES.PROXIMAL_COLON.ENTEROCYTES": "HOXB6", + "LARGE_INTESTINES.PROXIMAL_COLON.GOBLET_CELLS": "HOXB6", + "LARGE_INTESTINES.PROXIMAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "HOXB6", + "LARGE_INTESTINES.PROXIMAL_COLON.TUFT_CELLS": "HOXB6", + "LARGE_INTESTINES.PROXIMAL_COLON.PROLIFERATING_STEM": "LGR5", + "LARGE_INTESTINES.DISTAL_COLON.ENTEROCYTES": "HOXB13", + "LARGE_INTESTINES.DISTAL_COLON.GOBLET_CELLS": "HOXB13", + "LARGE_INTESTINES.DISTAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "HOXB13", + "LARGE_INTESTINES.DISTAL_COLON.TUFT_CELLS": "HOXB13", + "LARGE_INTESTINES.DISTAL_COLON.PROLIFERATING_STEM": "LGR5", + "LIMB_MUSCLE.SATELLITE_CELLS_1.NA": "VCAM1", + "LIMB_MUSCLE.SATELLITE_CELLS_2.NA": "VCAM1", + "LIMB_MUSCLE.IMMUNE.MACROPHAGE": "PTPRC", + "LIMB_MUSCLE.IMMUNE.T_CELL": "PTPRC", + "LIMB_MUSCLE.IMMUNE.B_CELL": "PTPRC", + "LIMB_MUSCLE.NA.MESENCYHMAL_STEM_CELLS_MSC": "ATN1", + "LIMB_MUSCLE.NA.ENOTHELIAL": "PECAM1", + "LIMB_MUSCLE.NA.CHONDROCYTES_OR_MSC_PROGENITORS": "CHODL", + "DIAPHRAM.SATELLITE_CELLS.NA": "PAX7", + "DIAPHRAM.FIBRO_ADIOPEGNIC_PROGENITORS_MSC.NA": "PDGFRA", + "DIAPHRAM.ENDOTHELIAL_CELLS.NA": "PECAM1", + "DIAPHRAM.IMMUNE.B_CELLS": "CD19", + "DIAPHRAM.IMMUNE.T_CELLS": "CD19", + "DIAPHRAM.IMMUNE.MACROPHAGE": "ITGAM", + "SKIN.INTERFOLLICULAR_EPIDERMIS.STEM_CELL": "KRT14", + "SKIN.INTERFOLLICULAR_EPIDERMIS.ACTIVELY_DIVIDNG_STEM_CELLS": "TOP2A", + "SKIN.INTERFOLLICULAR_EPIDERMIS.DIFFERENTIATED_PROGENY": "KRT10", + "SKIN.BULGE_CELLS.OUTER_BULGE": "DKK3", + "SKIN.BULGE_CELLS.INNER_BULGE": "FGF18", + "MAMMARY_GLAND.EPITHELIAL_CELLS.T_CELLS": "CD3E", + "MAMMARY_GLAND.EPITHELIAL_CELLS.B_CELLS": "CD74", + "MAMMARY_GLAND.EPITHELIAL_CELLS.MACROPHAGES": "CD74", + "MAMMARY_GLAND.EPITHELIAL_CELLS.BASAL": "KRT14", + "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL": "KRT8", + "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL_PROGENITORS": "KRT8", + "MAMMARY_GLAND.EPITHELIAL_CELLS.HORMONE_RESPONSIVE_LUMINAL": "KRT8", + "MAMMARY_GLAND.ENDOTHELIAL_CELLS.NA": "ESAM", + "MAMMARY_GLAND.STROMAL_CELLS.NA": "VIM", + "THYMUS.IMMUNE.DN1_THYMOCYTES": "CD44", + "THYMUS.IMMUNE.DP_CELLS": "DNTT", + "THYMUS.IMMUNE.IMMUNE": "CD8B1", + "THYMUS.IMMUNE.PROLIFERATING_THYMOCYTES": "TOP2A", + "THYMUS.STROMAL_CELLS.LYMPHOCYTE": "ZBTB7B", + "THYMUS.STROMAL_CELLS.STROMAL_CELLS": "CD3E", + "THYMUS.STROMAL_CELLS.DENDRITIC_CELLS": "PTPRC", + "THYMUS.STROMAL_CELLS.MESENCHYMAL_CELLS": "IGFBP7", + "THYMUS.STROMAL_CELLS.THYMIC_EPITHELIAL_CELLS": "KRT5", + "BRAIN.MICROGLIA.NA": "CX3CR1", + "BRAIN.NON_PARENCHYMAL_MACROPHAGES.NA": "CX3CR1", + "BRAIN.OLIGODENDROCYTE_PROGENITOR_CELLS.NA": "PDGFRA", + "BRAIN.MATURE_MYELINATING_OLIGODENDROCYTES.NA": "MOG", + "BRAIN.BRAIN_ENDOTHELIAL_CELLS.NA": "PECAM1", + "BRAIN.ASTROCYTE.NA": "ALDH1L1", + "BRAIN.BERGMAN_GLIA.NA": "GDF10", + "BRAIN.EXCITATORY_NEURONS.NA": "SLC17A7", + "BRAIN.INHIBITORY_NEURON.NA": "GAD1" + }, + { + "BLADDER.EPITHELIAL_UROTHELIAL.UMBRELLA_CELL": "UPK3A", + "BLADDER.EPITHELIAL_UROTHELIAL.BASAL_CELL": "KRT5", + "BLADDER.MESENCHYMAL.NA": "CAR3", + "FAT.NA.MESENCHYMAL_PROGENITORS": "CD34", + "FAT.IMMUNE_CELLS.B_CELLS": "PTPRC", + "FAT.IMMUNE_CELLS.T_CELLS": "CD8A", + "FAT.IMMUNE_CELLS.NK_CELLS": "GZMA", + "FAT.IMMUNE_CELLS.MYELOID": "CD68", + "FAT.NA.ENDOTHELIAL_CELLS": "CDH5", + "HEART_AND_AORTA.VASCULAR_ENDOTHELIAL.NA": "CDH5", + "HEART_AND_AORTA.FIBROBLASTS.NA": "COL3A1", + "HEART_AND_AORTA.ATRIAL_CARDIOMYOCYTES.NA": "MYL7", + "HEART_AND_AORTA.ENDOCARDIAL.NA": "PECAM1", + "HEART_AND_AORTA.IMMUNE.NA": "H2-EB1", + "HEART_AND_AORTA.MYOFIBROBLASTS.NA": "", + "HEART_AND_AORTA.SMOOTH_MUSCLE.NA": "ACTA2", + "HEART_AND_AORTA.CARDIOMYOCYTES.NA": "", + "HEART_AND_AORTA.AORTIC_ENDOTHELIAL.NA": "", + "HEART_AND_AORTA.ENDOTHELIAL.NA": "PECAM1", + "HEART_AND_AORTA.ANTIGEN_PRESENTING.NA": "H2-EB1", + "HEART_AND_AORTA.MACROPHAGES.NA": "CD14", + "KIDNEY.FENESTRATED_ENDOTHELIAL_CELLS.NA": "", + "KIDNEY.MESANGIAL_CELLS.NA": "VIM", + "KIDNEY.PODOCYTES.NA": "WT1", + "KIDNEY.TUBULE.PROXIMAL_BRUSH_BORDER_CELLS": "", + "KIDNEY.TUBULE.DISTAL_COLLECTING_DUCT_PRINCIPAL_CELLS": "SCNN1A", + "PANCREAS.EXOCRINE.ACINAR_CELLS": "CPA1", + "PANCREAS.EXOCRINE.DUCTAL_CELLS": "HNF1B", + "PANCREAS.ENDOCRINE.BETA": "INS2", + "PANCREAS.ENDOCRINE.ALPHA": "MAFB", + "PANCREAS.ENDOCRINE.DELTA": "HHEX", + "PANCREAS.ENDOCRINE.PP": "HNF1B", + "PANCREAS.NA.ENDOTHELIAL": "PECAM1", + "PANCREAS.NA.IMMUNE": "", + "PANCREAS.NA.STELLATE_CELLS": "PDGFRB", + "SPLEEN.IMMUNE.B_CELLS": "CCR2", + "SPLEEN.IMMUNE.T_CELLS": "CD8B1", + "TRACHEA.EPITHELIUM.CILIATED": "CDH1", + "TRACHEA.EPITHELIUM.SECRETORY": "CDH1", + "TRACHEA.EPITHELIUM.NEUROENDOCRINE": "CDH1", + "TRACHEA.EPITHELIUM.BASAL": "CDH1", + "TRACHEA.NA.MESENCHYMAL": "COL1A1", + "TRACHEA.NA.IMMUNE": "", + "TRACHEA.NA.ENDOTHELIAL": "", + "TONGUE.EPITHELIUM.PROLIFERATIVE_BASAL": "CDC20", + "TONGUE.EPITHELIUM.BASAL_KERATINOCYTES": "SBSN", + "TONGUE.EPITHELIUM.SUPRABASAL_BASAL_KERATINOCYTES": "KRT10", + "TONGUE.EPITHELIUM.FILIFORM_ASSOCIATED_KERATINOCYTES": "KRT36", + "TONGUE.EPITHELIUM.TASTE_RECEPTOR_CELLS": "KRT19", + "MARROW.WHOLE_MARROW.T_CELLS": "THY1", + "MARROW.WHOLE_MARROW.NK_CELLS": "KLRB1C", + "MARROW.WHOLE_MARROW.NKT_CELLS": "THY1", + "MARROW.WHOLE_MARROW.IMMATURE_T_CELLS": "CD4", + "MARROW.WHOLE_MARROW.IMMATURE_NK": "KLRB1C", + "MARROW.WHOLE_MARROW.IMMATURE_NKT": "CD4", + "MARROW.WHOLE_MARROW.PRE_NK": "STMN1", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.PRO_B": "RAG1", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.LATE_PRO_B": "RAG1", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.IMMATURE_B": "CD79A", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.MATURE_NAIVE_B": "CD79B", + "MARROW.TER119_B220_FACTION.LATE_PRO_B": "PAX5", + "MARROW.TER119_B220_FACTION.INTERMEDIATE_PRE_B": "RAG1", + "MARROW.TER119_B220_FACTION.IMMATURE_B": "CD19", + "MARROW.TER119_B220_FACTION.MATURE_NAIVE_B": "CD19", + "MARROW.UNFRACTIONED_MARROW.HEMATOPOIETIC_PRECURSOR_CELLS": "STMN1", + "MARROW.UNFRACTIONED_MARROW.PROERYTHOBLASTS": "MKI67", + "MARROW.UNFRACTIONED_MARROW.ERYTHOBLASTS": "", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_GRANULOPOIETIC_CELLS": "PGLYRP1", + "MARROW.UNFRACTIONED_MARROW.GRANULOCYTES": "PGLYRP1", + "MARROW.UNFRACTIONED_MARROW.BASOPHILS": "FCER1A", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_PROMONOCYTE": "MPEG1", + "MARROW.UNFRACTIONED_MARROW.MATURE_MONOCYTES": "MPEG1", + "MARROW.UNFRACTIONED_MARROW.BM_MACROPHAGES": "MPEG1", + "MARROW.SUBFRACTIONATION.HPC_CLUSTERS": "GPR56", + "MARROW.SUBFRACTIONATION.QUIESCENT_HSC_ENRICHED_FRACTION": "FLT3", + "MARROW.SUBFRACTIONATION.MPPS": "MKI67", + "MARROW.SUBFRACTIONATION.MEGAKARYOCYTE_ERYTHROCYTE_PROGENITOR": "KLF1", + "MARROW.SUBFRACTIONATION.COMMON_LYMPHOCYTE_PROGENITOR_LINEAGE": "LY6C2", + "MARROW.MYELOID_CELLS.GRANULOCYTE_MONOCYTE_PROGENITORS": "KIT", + 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"MARROW.UNFRACTIONED_FRACTIONATED_MARROW.PRO_B": "", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.LATE_PRO_B": "", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.IMMATURE_B": "", + "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.MATURE_NAIVE_B": "", + "MARROW.TER119_B220_FACTION.LATE_PRO_B": "", + "MARROW.TER119_B220_FACTION.INTERMEDIATE_PRE_B": "", + "MARROW.TER119_B220_FACTION.IMMATURE_B": "", + "MARROW.TER119_B220_FACTION.MATURE_NAIVE_B": "", + "MARROW.UNFRACTIONED_MARROW.HEMATOPOIETIC_PRECURSOR_CELLS": "", + "MARROW.UNFRACTIONED_MARROW.PROERYTHOBLASTS": "", + "MARROW.UNFRACTIONED_MARROW.ERYTHOBLASTS": "", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_GRANULOPOIETIC_CELLS": "", + "MARROW.UNFRACTIONED_MARROW.GRANULOCYTES": "", + "MARROW.UNFRACTIONED_MARROW.BASOPHILS": "", + "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_PROMONOCYTE": "", + "MARROW.UNFRACTIONED_MARROW.MATURE_MONOCYTES": "", + "MARROW.UNFRACTIONED_MARROW.BM_MACROPHAGES": "", + "MARROW.SUBFRACTIONATION.HPC_CLUSTERS": "", + "MARROW.SUBFRACTIONATION.QUIESCENT_HSC_ENRICHED_FRACTION": "", + "MARROW.SUBFRACTIONATION.MPPS": "", + "MARROW.SUBFRACTIONATION.MEGAKARYOCYTE_ERYTHROCYTE_PROGENITOR": "", + "MARROW.SUBFRACTIONATION.COMMON_LYMPHOCYTE_PROGENITOR_LINEAGE": "", + "MARROW.MYELOID_CELLS.GRANULOCYTE_MONOCYTE_PROGENITORS": "", + "MARROW.MYELOID_CELLS.MATURE_MONOCYTES": "", + "MARROW.MYELOID_CELLS.MACROPHAGES": "", + "MARROW.MYELOID_CELLS.GRANULOCYTE_1": "", + "MARROW.MYELOID_CELLS.GRANULOCYTE_2_BASOPHILS": "", + "LUNG.EPITHELIAL.MULTICILIATED": "", + "LUNG.EPITHELIAL.ALVEOLAR_TYPE_2": "", + "LUNG.ENDOTHELIAL.NA": "", + "LUNG.STROMAL.NA": "", + "LUNG.IMMUNE.ALVEOLAR_MACROPHAGES": "", + "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGES": "", + "LUNG.IMMUNE.DENDRITIC_CELLS": "", + "LUNG.IMMUNE.INVADING_MONOCYTES": "", + "LUNG.IMMUNE.NON_CANONICAL_1": "", + "LUNG.IMMUNE.NON_CANONICAL_2": "", + "LUNG.STROMA.ADVENTITIAL_FIBROBLAST": "", + "LUNG.STROMA.SCA1_ADVENTITIAL_FIBROBLAST": "", + "LUNG.STROMA.ALVEOLAR_FIBROBLAST": "", + "LUNG.STROMA.MESOTHELIAL_CELL": "", + "LUNG.STROMA.MYOFIBROBLAST": "", + "LUNG.STROMA.PERICYTE": "", + "LUNG.STROMA.SMOOTH_MUSCLE_CELL": "", + "LUNG.STROMA.CHONDROCYTE": "", + "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_1_CELL": "", + "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_2_CELL": "", + "LUNG.EPITHELIUM.CILIATED_CELL": "", + "LUNG.EPITHELIUM.NEUROENDOCRINE_CELL": "", + "LUNG.EPITHELIUM.BASAL_CELL": "", + "LUNG.EPITHELIUM.CLUB_CELL": "", + "LUNG.EPITHELIUM.GOBLET_CELL": "", + "LUNG.IMMUNE.ALVEOLAR_MACROPHAGE": "", + "LUNG.IMMUNE.B_CELL": "", + "LUNG.IMMUNE.BASOPHIL": "", + "LUNG.IMMUNE.CLASSICAL_MONOCYTE": "", + "LUNG.IMMUNE.DENDRITIC_CELL": "", + "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGE": "", + "LUNG.IMMUNE.NATURAL_KILLER_CELL": "", + "LUNG.IMMUNE.NEUTROPHIL": "", + "LUNG.IMMUNE.NONCLASSICAL_MONOCYTE": "", + "LUNG.IMMUNE.CD4_T_CELL": "", + "LUNG.IMMUNE.CD8_T_CELL": "", + "LUNG.IMMUNE.INTERMEDIATE_MONOCYTE": "", + "LUNG.IMMUNE.NATURAL_KILLER_T_CELL": "", + "LUNG.IMMUNE.PLASMACYTOID_DENDRITIC_CELL": "", + "LUNG.IMMUNE.PROLIFERATING_ALVEOLAR_MACROPHAGE": "", + "LUNG.IMMUNE.PROLIFERATING_NK_T_CELL": "", + "LUNG.ENDOTHELIUM.ARTERY_CELL": "", + "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_1_CELL": "", + "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_2_CELL": "", + "LUNG.ENDOTHELIUM.LYMPHATIC_CELL": "", + "LUNG.ENDOTHELIUM.VEIN_CELL": "", + "LUNG.NEURONAL_GLIA.GLIAL_CELL": "", + "LIVER.NA.ENDOTHELIUM": "", + "LIVER.NA.STELLATE_CELLS": "", + "LIVER.HEPATOCYTES.PERICENTRAL_PERIPORTAL_MIDLOBULAR": "UBB", + "LIVER.IMMUNE.KUPFFER_MACROPHAGE": "", + "LIVER.IMMUNE.NK_NKT_CELLS": "", + "LIVER.IMMUNE.CIRCULATING_B_CELLS": "", + "LIVER.IMMUNE.MACROPHAGES_MONOCYTES": "", + "LIVER.IMMUNE.T_CELLS": "", + "LIVER.CHOLANGIOCYTES_BILE_DUCT_EPITHELIAL_CELLS.NA": "", + "LIVER.IMMUNE.NEUTROPHILS": "", + "LIVER.IMMUNE.PLASMACYTOID_DENDRITIC": "", + "LIVER.ERYTHROCYTES.NA": "", + "LARGE_INTESTINES.PROXIMAL_COLON.ENTEROCYTES": "", + "LARGE_INTESTINES.PROXIMAL_COLON.GOBLET_CELLS": "", + "LARGE_INTESTINES.PROXIMAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "", + "LARGE_INTESTINES.PROXIMAL_COLON.TUFT_CELLS": "", + "LARGE_INTESTINES.PROXIMAL_COLON.PROLIFERATING_STEM": "", + "LARGE_INTESTINES.DISTAL_COLON.ENTEROCYTES": "", + "LARGE_INTESTINES.DISTAL_COLON.GOBLET_CELLS": "", + "LARGE_INTESTINES.DISTAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "", + "LARGE_INTESTINES.DISTAL_COLON.TUFT_CELLS": "", + "LARGE_INTESTINES.DISTAL_COLON.PROLIFERATING_STEM": "", + "LIMB_MUSCLE.SATELLITE_CELLS_1.NA": "", + "LIMB_MUSCLE.SATELLITE_CELLS_2.NA": "", + "LIMB_MUSCLE.IMMUNE.MACROPHAGE": "", + "LIMB_MUSCLE.IMMUNE.T_CELL": "", + "LIMB_MUSCLE.IMMUNE.B_CELL": "", + "LIMB_MUSCLE.NA.MESENCYHMAL_STEM_CELLS_MSC": "", + "LIMB_MUSCLE.NA.ENOTHELIAL": "", + "LIMB_MUSCLE.NA.CHONDROCYTES_OR_MSC_PROGENITORS": "", + "DIAPHRAM.SATELLITE_CELLS.NA": "", + "DIAPHRAM.FIBRO_ADIOPEGNIC_PROGENITORS_MSC.NA": "", + "DIAPHRAM.ENDOTHELIAL_CELLS.NA": "", + "DIAPHRAM.IMMUNE.B_CELLS": "", + "DIAPHRAM.IMMUNE.T_CELLS": "", + "DIAPHRAM.IMMUNE.MACROPHAGE": "", + "SKIN.INTERFOLLICULAR_EPIDERMIS.STEM_CELL": "", + "SKIN.INTERFOLLICULAR_EPIDERMIS.ACTIVELY_DIVIDNG_STEM_CELLS": "", + "SKIN.INTERFOLLICULAR_EPIDERMIS.DIFFERENTIATED_PROGENY": "", + "SKIN.BULGE_CELLS.OUTER_BULGE": "", + "SKIN.BULGE_CELLS.INNER_BULGE": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.T_CELLS": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.B_CELLS": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.MACROPHAGES": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.BASAL": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL_PROGENITORS": "", + "MAMMARY_GLAND.EPITHELIAL_CELLS.HORMONE_RESPONSIVE_LUMINAL": "", + "MAMMARY_GLAND.ENDOTHELIAL_CELLS.NA": "", + "MAMMARY_GLAND.STROMAL_CELLS.NA": "", + "THYMUS.IMMUNE.DN1_THYMOCYTES": "", + "THYMUS.IMMUNE.DP_CELLS": "", + "THYMUS.IMMUNE.IMMUNE": "", + "THYMUS.IMMUNE.PROLIFERATING_THYMOCYTES": "", + "THYMUS.STROMAL_CELLS.LYMPHOCYTE": "", + "THYMUS.STROMAL_CELLS.STROMAL_CELLS": "", + "THYMUS.STROMAL_CELLS.DENDRITIC_CELLS": "", + "THYMUS.STROMAL_CELLS.MESENCHYMAL_CELLS": "", + "THYMUS.STROMAL_CELLS.THYMIC_EPITHELIAL_CELLS": "", + "BRAIN.MICROGLIA.NA": "", + "BRAIN.NON_PARENCHYMAL_MACROPHAGES.NA": "", + "BRAIN.OLIGODENDROCYTE_PROGENITOR_CELLS.NA": "", + "BRAIN.MATURE_MYELINATING_OLIGODENDROCYTES.NA": "", + "BRAIN.BRAIN_ENDOTHELIAL_CELLS.NA": "", + "BRAIN.ASTROCYTE.NA": "", + "BRAIN.BERGMAN_GLIA.NA": "", + "BRAIN.EXCITATORY_NEURONS.NA": "", + "BRAIN.INHIBITORY_NEURON.NA": "" + } +]; + +const testGeneSets = {}; + +_.forEach(_testGeneSets[0], (gene, set) => { + testGeneSets[set] = []; +}); + +_.forEach(_testGeneSets, pairs => { + _.forEach(pairs, (gene, set) => { + if (gene !== "") { + testGeneSets[set].push(gene); + } + }); +}); + +export default testGeneSets;