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Tie2; human ortholog: TEK.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"pecam1","protein":"pecam1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PECAM1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_hemogenic_endothelium","name":"Hemogenic endothelium (zebrafish)","parent":"model_organisms.zf_endothelial","synonyms":[],"cl_id":null,"tissues":["ventral wall of dorsal aorta"],"description":"Aortic endothelial subset that undergoes endothelial-to-hematopoietic transition.","markers":[{"gene":"runx1","protein":"runx1","modality":["mRNA","protein"],"methods":["ISH","reporter","lineage-tracing"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: RUNX1.","refs":["PMID:20154733"],"evidence":"direct","tier":"cited"},{"gene":"cmyb","protein":"cmyb","modality":["mRNA"],"methods":["ISH","reporter"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: MYB.","refs":["PMID:20154733"],"evidence":"direct","tier":"cited"},{"gene":"kdrl","protein":"kdrl","modality":["mRNA"],"methods":["reporter"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: KDR.","refs":["PMID:20154733"],"evidence":"direct","tier":"cited"},{"gene":"gata2b","protein":"gata2b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: GATA2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"cdh5","protein":"cdh5","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: CDH5.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_lymphatic_endothelial","name":"Lymphatic endothelial cell (zebrafish)","parent":"model_organisms.zf_endothelial","synonyms":[],"cl_id":null,"tissues":["lymphatic vessels","trunk"],"description":"Lymphatic lineage of the zebrafish vasculature.","markers":[{"gene":"prox1a","protein":"prox1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PROX1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"flt4","protein":"flt4","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Vegfr3; human ortholog: FLT4.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"lyve1b","protein":"lyve1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: LYVE1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"mrc1a","protein":"mrc1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: MRC1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"stab2","protein":"stab2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Also scavenger endothelium; human ortholog: STAB2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_cardiomyocyte","name":"Cardiomyocyte (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["heart"],"description":"Contractile cells of the zebrafish heart.","markers":[{"gene":"myl7","protein":"myl7","modality":["mRNA","protein"],"methods":["reporter","ISH"],"polarity":"+","specificity":"defining","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. cmlc2 promoter drives myocardium-specific GFP; human ortholog: MYL7.","refs":["PMID:12950077"],"evidence":"direct","tier":"cited"},{"gene":"nkx2.5","protein":"nkx2.5","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: NKX2-5.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tnnt2a","protein":"tnnt2a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TNNT2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"vmhc","protein":"vmhc","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Ventricular myosin heavy chain; human ortholog: MYH7-like.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"myh6","protein":"myh6","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Atrial myosin heavy chain (amhc); human ortholog: MYH6.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"hand2","protein":"hand2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: HAND2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_epicardial","name":"Epicardial cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["heart"],"description":"Outer mesothelial layer of the heart, activated upon injury.","markers":[{"gene":"tcf21","protein":"tcf21","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TCF21.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tbx18","protein":"tbx18","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TBX18.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"wt1b","protein":"wt1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: WT1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"aldh1a2","protein":"aldh1a2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: ALDH1A2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_hair_cell","name":"Neuromast hair cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["lateral line neuromast","inner ear"],"description":"Mechanosensory hair cell of lateral line and ear.","markers":[{"gene":"atoh1a","protein":"atoh1a","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Proneural bHLH required for hair cell fate in the ear; human ortholog: ATOH1.","refs":["PMID:17166920"],"evidence":"direct","check":"partial","tier":"cited"},{"gene":"myo6b","protein":"myo6b","modality":["mRNA","protein"],"methods":["scRNA-seq","reporter"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: MYO6.","refs":["PMID:30681411"],"evidence":"atlas","tier":"cited"},{"gene":"pou4f3","protein":"pou4f3","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: POU4F3.","refs":["PMID:30681411"],"evidence":"atlas","tier":"cited"},{"gene":"cdh23","protein":"cdh23","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: CDH23.","refs":["PMID:30681411"],"evidence":"atlas","tier":"cited"},{"gene":"tmc2b","protein":"tmc2b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. 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UV opsin; human ortholog: OPN1SW.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"pde6c","protein":"pde6c","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PDE6C.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"thrb","protein":"thrb","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. 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Human ortholog: RLBP1.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"gfap","protein":"gfap","modality":["mRNA","protein"],"methods":["scRNA-seq","IF"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: GFAP.","refs":["PMID:33004674","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tuba1a","protein":"tuba1a","modality":["mRNA"],"methods":["reporter"],"polarity":"+","specificity":"subset","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. alpha1-tubulin promoter activated in injury-reactive Müller glia; human ortholog: TUBA1A.","refs":["PMID:16763038"],"evidence":"direct","check":"partial","tier":"cited"},{"gene":"sox2","protein":"sox2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SOX2.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"apoeb","protein":"apoeb","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: APOE.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_rgc","name":"Retinal ganglion cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["retina"],"description":"Projection neurons of the retina.","markers":[{"gene":"atoh7","protein":"atoh7","modality":["mRNA"],"methods":["scRNA-seq","ISH"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Determinant of RGC lineage; human ortholog: ATOH7.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"isl2b","protein":"isl2b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: ISL2.","refs":["PMID:33004674","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"elavl4","protein":"elavl4","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: ELAVL4.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"rbpms2b","protein":"rbpms2b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: RBPMS2.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"pou4f1","protein":"pou4f1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: POU4F1 (BRN3A).","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_retinal_progenitor","name":"Retinal progenitor cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["retina"],"description":"Multipotent progenitors of the developing retina.","markers":[{"gene":"vsx2","protein":"vsx2","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: VSX2.","refs":["PMID:31782996","PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"rx1","protein":"rx1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: RAX.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"pax6a","protein":"pax6a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PAX6.","refs":["PMID:31782996","PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"sox2","protein":"sox2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SOX2.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"},{"gene":"her4.1","protein":"her4.1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Notch target; human ortholog: HES family.","refs":["PMID:33004674"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_rpe","name":"Retinal pigment epithelium (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["retina"],"description":"Pigmented epithelium supporting photoreceptors.","markers":[{"gene":"rpe65a","protein":"rpe65a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"defining","compartment":"ER","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: RPE65.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tyrp1b","protein":"tyrp1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"mitochondrial","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TYRP1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"pmela","protein":"pmela","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"other","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PMEL.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"dct","protein":"dct","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"other","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: DCT.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_oligodendrocyte","name":"Oligodendrocyte (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["CNS","spinal cord"],"description":"Myelinating glia of the CNS.","markers":[{"gene":"olig2","protein":"olig2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Also motor neuron progenitors; human ortholog: OLIG2.","refs":["PMID:31782996","PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"sox10","protein":"sox10","modality":["mRNA"],"methods":["scRNA-seq","reporter"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SOX10.","refs":["PMID:11684650"],"evidence":"direct","tier":"cited"},{"gene":"mbpa","protein":"mbpa","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: MBP.","refs":["PMID:31782996","PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"mpz","protein":"mpz","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Mostly PNS; human ortholog: MPZ.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"plp1b","protein":"plp1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PLP1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_radial_glia","name":"Radial glia / neural progenitor (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["brain","spinal cord"],"description":"Neural stem/progenitor cells of the zebrafish CNS.","markers":[{"gene":"gfap","protein":"gfap","modality":["mRNA","protein"],"methods":["scRNA-seq","IF"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: GFAP.","refs":["PMID:29608178","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"her4.1","protein":"her4.1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: HES family.","refs":["PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"sox2","protein":"sox2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SOX2.","refs":["PMID:29608178","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"fabp7a","protein":"fabp7a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: FABP7.","refs":["PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"cx43","protein":"cx43","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Gap junction gja1; human ortholog: GJA1.","refs":["PMID:29608178"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_neuron_pan","name":"Post-mitotic neuron (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["CNS"],"description":"Differentiated neurons marked by elavl3 and neurod family.","markers":[{"gene":"elavl3","protein":"elavl3","modality":["mRNA"],"methods":["scRNA-seq","ISH"],"polarity":"+","specificity":"pan-lineage","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. HuC; human ortholog: ELAVL3.","refs":["PMID:31782996","PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"neurod1","protein":"neurod1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: NEUROD1.","refs":["PMID:31782996","PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"snap25a","protein":"snap25a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"pan-lineage","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SNAP25.","refs":["PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"syt1a","protein":"syt1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"pan-lineage","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SYT1.","refs":["PMID:29608178"],"evidence":"atlas","tier":"cited"},{"gene":"stmn2a","protein":"stmn2a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"pan-lineage","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: STMN2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_neural_crest","name":"Neural crest cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["neural crest","embryo"],"description":"Multipotent migratory crest population.","markers":[{"gene":"sox10","protein":"sox10","modality":["mRNA","protein"],"methods":["ISH","reporter"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. colourless mutants show loss of non-ectomesenchymal crest derivatives; human ortholog: SOX10.","refs":["PMID:11684650"],"evidence":"direct","tier":"cited"},{"gene":"foxd3","protein":"foxd3","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: FOXD3.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tfap2a","protein":"tfap2a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TFAP2A.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"crestin","protein":"crestin","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"other","species":["zebrafish"],"notes":"Danio rerio. Zebrafish-specific crest transcript; no human ortholog.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"snai2","protein":"snai2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SNAI2.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"sox9b","protein":"sox9b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SOX9.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_melanophore","name":"Melanophore / melanocyte (zebrafish)","parent":"model_organisms.zf_neural_crest","synonyms":[],"cl_id":null,"tissues":["skin","stripes"],"description":"Black pigment cells.","markers":[{"gene":"mitfa","protein":"mitfa","modality":["mRNA","protein"],"methods":["ISH","reporter","functional"],"polarity":"+","specificity":"defining","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. nacre mutant lacks melanophores; human ortholog: MITF.","refs":["PMID:10433906"],"evidence":"direct","check":"partial","tier":"cited"},{"gene":"dct","protein":"dct","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"other","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: DCT.","refs":["PMID:31140974"],"evidence":"atlas","tier":"cited"},{"gene":"tyrp1b","protein":"tyrp1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"mitochondrial","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TYRP1.","refs":["PMID:31140974"],"evidence":"atlas","tier":"cited"},{"gene":"pmela","protein":"pmela","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"other","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PMEL.","refs":["PMID:31140974"],"evidence":"atlas","tier":"cited"},{"gene":"tyr","protein":"tyr","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"mitochondrial","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: TYR.","refs":["PMID:31140974"],"evidence":"atlas","tier":"cited"},{"gene":"kita","protein":"kita","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: KIT.","refs":["PMID:31140974"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_xanthophore","name":"Xanthophore (zebrafish)","parent":"model_organisms.zf_neural_crest","synonyms":[],"cl_id":null,"tissues":["skin","stripes"],"description":"Yellow/orange pigment cells.","markers":[{"gene":"csf1ra","protein":"csf1ra","modality":["mRNA","protein"],"methods":["reporter","functional"],"polarity":"+","specificity":"defining","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. 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Fast muscle; human ortholog: MYLPF.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"acta1a","protein":"acta1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: ACTA1.","refs":["PMID:29700229","PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"myhz1.1","protein":"myhz1.1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Fast myosin heavy chain; human ortholog: MYH family.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"smyhc1","protein":"smyhc1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"subset","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Slow myosin heavy chain; human ortholog: MYH7B-like.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_beta_cell","name":"Pancreatic beta cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["pancreas islet"],"description":"Insulin-producing cells.","markers":[{"gene":"ins","protein":"ins","modality":["mRNA","protein"],"methods":["reporter","ISH","IF"],"polarity":"+","specificity":"defining","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. ins promoter drives nitroreductase for beta-cell ablation; human ortholog: INS.","refs":["PMID:17223324"],"evidence":"direct","tier":"cited"},{"gene":"pdx1","protein":"pdx1","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PDX1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"nkx6.1","protein":"nkx6.1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: NKX6-1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"gcga","protein":"gcga","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"-","specificity":"negative-exclusion","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. 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Carboxypeptidase; human ortholog: CPA family.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"prss1","protein":"prss1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: PRSS1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"ctrb1","protein":"ctrb1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: CTRB1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_hepatocyte","name":"Hepatocyte (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["liver"],"description":"Liver parenchymal cells.","markers":[{"gene":"fabp10a","protein":"fabp10a","modality":["mRNA"],"methods":["ISH","scRNA-seq"],"polarity":"+","specificity":"defining","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Liver fatty acid-binding protein; human ortholog: FABP1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"apoa1a","protein":"apoa1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: APOA1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"tfa","protein":"tfa","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Transferrin-a; human ortholog: TF.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"cp","protein":"cp","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Ceruloplasmin; human ortholog: CP.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"hnf4a","protein":"hnf4a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: HNF4A.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_enterocyte","name":"Intestinal epithelial cell / enterocyte (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["intestine"],"description":"Absorptive intestinal epithelium.","markers":[{"gene":"fabp2","protein":"fabp2","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: FABP2.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"cdx1b","protein":"cdx1b","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: CDX1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"apoa4b.1","protein":"apoa4b.1","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"secreted","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: APOA4.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"epcam","protein":"epcam","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"pan-lineage","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: EPCAM.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"}],"lineage":"model_organisms"},{"id":"model_organisms.zf_kidney_proximal","name":"Pronephric proximal tubule cell (zebrafish)","parent":"model_organisms.zf","synonyms":[],"cl_id":null,"tissues":["pronephros"],"description":"Proximal tubule epithelium of the larval kidney.","markers":[{"gene":"slc20a1a","protein":"slc20a1a","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. Human ortholog: SLC20A1.","refs":["PMID:31782996"],"evidence":"atlas","tier":"cited"},{"gene":"cdh17","protein":"cdh17","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"surface","species":["zebrafish"],"notes":"Danio rerio. 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Deadpan; human ortholog: HES family (approx.).","refs":["PMID:31746739","PMID:16549393"],"evidence":"atlas","check":"partial","tier":"cited"},{"gene":"mira","protein":"mira","modality":["mRNA","protein"],"methods":["IF","scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["other"],"notes":"Drosophila melanogaster. Miranda cargo adaptor; asymmetrically localised.","refs":["PMID:16549393","PMID:31746739"],"evidence":"atlas","check":"not_found","tier":"cited"},{"gene":"wor","protein":"wor","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["other"],"notes":"Drosophila melanogaster. Worniu; Snail family.","refs":["PMID:31746739"],"evidence":"atlas","check":"not_found","tier":"cited"},{"gene":"ase","protein":"ase","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"nuclear","species":["other"],"notes":"Drosophila melanogaster. Asense; human ortholog: ASCL1 (approx.).","refs":["PMID:31746739"],"evidence":"atlas","check":"not_found","tier":"cited"},{"gene":"insc","protein":"insc","modality":["mRNA"],"methods":["scRNA-seq"],"polarity":"+","specificity":"enriched","compartment":"cytoplasmic","species":["other"],"notes":"Drosophila melanogaster. Inscuteable.","refs":["PMID:31746739"],"evidence":"atlas","check":"not_found","tier":"cited"},{"gene":"elav","protein":"elav","modality":["mRNA","protein"],"methods":["IF"],"polarity":"-","specificity":"negative-exclusion","compartment":"nuclear","species":["other"],"notes":"Drosophila melanogaster. 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