The Cell Marker Accordion

A Web Tool for Single-Cell and Spatial Omics Annotation

The Cell Marker Accordion is a powerful and user-friendly platform designed to enhance the accuracy and interpretation of normal and aberrant cell populations in single-cell and spatial omics data. Our framework includes both a Shiny app and an R package.

The Cell Marker Accordion web interface allows users to easily explore the integrated built-in database of consistency-weighted markers. Specifically, it enables:

Search and download lists of cell types associated with input marker genes across different tissues in health and disease.

Search and download lists of cell types associated with input marker genes across different tissues in health and disease.

Integrate custom set of marker genes with the Cell Marker Accordion database.

Perform cell type marker enrichment analysis across tissues in health and disease.

Additionally, in all sections users can easily:

Browse hierarchies of cell types following the Cell Ontology structure in order to obtain the desired level of specificity in the markers in both search options.

Rank and select marker genes by their evidence consistency and specificity scores.

To perfom cell type annotation exploiting the comprehensive Cell Marker Accordion algorithm, we recommend using our R package

Encountering issues? Check out our GitHub page!

Search and download lists of marker genes by cell types across different tissues in health and disease

Info

Select species:

Condition

Tissue

Tissue aware

Cell type

See subtypes of:

Plot celltype_ID

Save Ontology plot

PNG PDF

Click on a node to look at cell type description

Zoom:

Table options Info

Table options Info

ECs

SPs

Table type

Simple

Complete

Merge subtypes

Yes

No

Download

CSV XLSX TSV

Search and download lists of cell types by marker genes across different tissues in health and disease

Info

Select species:

Insert marker genes

Upload file with marker genes

Condition

Tissue

Tissue aware

Plot celltype_ID

Save Ontology plot

PNG PDF

Click on a node to look at cell type description

Zoom:

Table options Info

ECs

SPs

Table type

Simple

Complete

Download

CSV XLSX TSV

Integrate custom set of marker genes with the Cell Marker Accordion database

Table type

Simple Complete

Download

CSV XLSX TSV

Filter the integrated database

Info

Select species:

Condition

Tissue

Tissue aware

Cell type

See subtypes of:

Plot celltype_ID

Save Ontology plot

PNG PDF

Click on a node to look at cell type description

Zoom:

Table options Info

Table options Info

ECs

SPs

Table type

Simple

Complete

Merge subtypes

Yes

No

Download

CSV XLSX TSV

Perform cell type marker enrichment analysis across tissues in health and disease

Info

Load file

InputFile

Specificy the number of positive genes to keep for each cluster

ALL

Specificy the number of negative genes to keep for each cluster

ALL

Type in number of positive genes

Type in number of negative genes

Add value

Add value

Load demo example

Output table generated by the FindAllMarkers function in the Seurat package

Filters Info

Select species:

Condition healthy ACTH-secreting pituitary adenoma Alzheimer's disease B-cell acute lymphoblastic leukemia B-cell lymphoma B-lymphoblastic leukemia/lymphoma COVID-19 Fanconi anemia Hodgkin's lymphoma Human papillomavirus infectious disease Lewy body dementia Parkinson's disease Pick's disease Sezary's disease T-cell acute lymphoblastic leukemia Zika fever acute kidney failure acute leukemia acute lymphoblastic leukemia acute monocytic leukemia acute myeloid leukemia adult T-cell leukemia/lymphoma adult hepatocellular carcinoma alcoholic hepatitis amyotrophic lateral sclerosis amyotrophic lateral sclerosis type 26 anaplastic large cell lymphoma biliary atresia blood platelet disease brain cancer brain ependymoma brain glioma central nervous system cancer cerebral primitive neuroectodermal tumor childhood ependymoma cholangiocarcinoma cholangiolocellular carcinoma chromophobe renal cell carcinoma chronic kidney disease chronic lymphocytic leukemia chronic myeloid leukemia chronic obstructive pulmonary disease clear cell renal cell carcinoma cystic fibrosis dementia diffuse glioma, H3 G34 mutant diffuse large B-cell lymphoma activated B-cell type diffuse midline glioma, H3 K27M-mutant epilepsy extrinsic allergic alveolitis follicular lymphoma frontotemporal dementia ganglioneuroma glioblastoma graft-versus-host disease hepatitis B hepatobiliary benign neoplasm hepatoblastoma hepatocellular carcinoma hepatosplenic T-cell lymphoma high grade glioma idiopathic pulmonary fibrosis insulinoma interstitial lung disease intracranial aneurysm intrahepatic cholangiocarcinoma intravascular large B-cell lymphoma kidney benign neoplasm kidney cancer large B-cell lymphoma leukemia low grade glioma lung adenocarcinoma lung cancer lung large cell carcinoma lung non-small cell carcinoma lung small cell carcinoma lung squamous cell carcinoma lupus nephritis lymphangioleiomyomatosis lymphoma major depressive disorder malaria malignant astrocytoma malignant peripheral nerve sheath tumor mantle cell lymphoma mature T-cell and NK-cell lymphoma medulloblastoma meningioma mixed fibrolamellar hepatocellular carcinoma mucinous tubular and spindle renal cell carcinoma multiple myeloma multiple sclerosis nephroblastoma nephrotic syndrome neuroblastoma non-Hodgkin lymphoma non-alcoholic fatty liver nonpapillary renal cell carcinoma nonspecific interstitial pneumonia obstructive sleep apnea oligodendroglioma pancreatic adenocarcinoma pancreatic cancer pancreatic ductal adenocarcinoma pancreatitis papillary renal cell carcinoma peripheral T-cell lymphoma pheochromocytoma pilocytic astrocytoma pituitary adenoma pituitary cancer pleomorphic carcinoma pneumonia portal hypertension primary biliary cholangitis primary mediastinal B-cell lymphoma primary sclerosing cholangitis progressive supranuclear palsy pulmonary emphysema pulmonary fibrosis pulmonary sarcoidosis pulmonary systemic sclerosis refractory hematologic cancer renal Wilms' tumor renal carcinoma renal cell carcinoma renal cell carcinoma with MiT translocations renal oncocytoma retinoblastoma sarcoidosis temporal lobe epilepsy type 1 diabetes mellitus allergic disease cerebellum cancer cerebrovascular disease cognitive disorder encephalomyelitis endocrine pancreas disease fibrosarcoma hypertensive encephalopathy inclusion body myopathy and brain white matter abnormalities kidney angiomyolipoma liver disease lymphadenitis malignant leptomeningeal neoplasm metabolic dysfunction-associated steatohepatitis motor neuron disease myeloproliferative neoplasm neurodegenerative disease neuropathy pulmonary hypertension schizophrenia supratentorial primitive neuroectodermal tumor type 2 diabetes mellitus viral infectious disease

Tissue alveolar system alveolus of lung anterior cingulate cortex arteriole of lymph node auditory cortex basal forebrain biliary ductule blood blood brain barrier blood plasma blood serum bone marrow brain bronchiole caudal ganglionic eminence caudate-putamen celiac lymph node central nervous system central vein of liver cerebellum cerebral cortex cerebrospinal fluid choroid plexus circumventricular organ collecting duct of renal tubule common iliac lymph node cortex of thymus cortical collecting duct deep inguinal lymph node descending thin limb distal convoluted tubule dorsal pancreatic duct dorsal root of spinal cord dorsolateral prefrontal cortex efferent lymphatic vessel endothelium of peritubular capillary enteric nervous system entorhinal cortex epithelium of bronchiole epithelium of lobar bronchus epithelium of respiratory bronchiole epithelium of segmental bronchus exocrine pancreas external iliac lymph node forebrain frontal cortex ganglion germinal center glomerular capillary endothelium glomerular mesangium glomerular parietal epithelium glomerular visceral epithelium gray matter of forebrain gray matter of hindbrain hepatic cord hepatic sinusoid high endothelial venule of lymph node hilum of lymph node hilum of spleen hippocampal formation hypothalamus ileocolic lymph node immune system inferior colliculus inner medulla of kidney insect embryonic brain intercalated duct of pancreas internal iliac lymph node intrahepatic bile duct juxtaglomerular apparatus kidney kidney blood vessel kidney interstitium kidney pyramid kidney vasculature lateral ganglionic eminence layer of developing cerebral cortex layer of neocortex liver liver blood vessel liver lobule liver perisinusoidal space lobar bronchus lobar bronchus mesenchyme lumbar spinal cord dorsal horn lumbar spinal cord lateral horn lumbar spinal cord ventral horn lumbar spinal cord white matter lung lung connective tissue lymph lymph node lymph node germinal center dark zone lymph node germinal center light zone lymph node germinal center mantle zone lymph node interfollicular cortex lymph node medullary cord lymph node medullary sinus lymph node paracortical cord lymph node paracortical sinus lymph node primary follicle lymph vasculature lymphatic capillary lymphatic vessel lymphatic vessel endothelium lymphoid tissue macula densa marginal zone of spleen medial ganglionic eminence medulla oblongata medulla of thymus medullary arteriole of lymph node medullary venule of lymph node meninx mesenteric lymph node mesocolic lymph node midbrain middle frontal gyrus neocortex nephron nerve nervous system neural tissue neuron projection bundle connecting eye with brain outer medullary collecting duct palatine tonsil pancreas pancreatic acinus pancreatic duct paraaortic lymph node penicillar arteriole periarterial lymphatic sheath peripheral nervous system pigmented layer of retina pituitary gland pons popliteal lymph node portal triad prefrontal cortex primary motor cortex pronephros proximal convoluted tubule segment 1 proximal convoluted tubule segment 2 proximal straight tubule proximal tubule pulmonary alveolar duct pulmonary alveolar parenchyma pulmonary capillary pulmonary interlobular septum pulmonary nerve plexus pulmonary vascular system red pulp of spleen renal afferent arteriole renal collecting system renal connecting tubule renal efferent arteriole renal glomerulus respiratory system lymphatic vessel endothelium retina segmental bronchus short descending thin limb smooth muscle tissue of bronchiole smooth muscle tissue of respiratory bronchiole smooth muscle tissue of terminal bronchiole somatosensory cortex spinal cord spleen spleen central arteriole spleen germinal center spleen perifollicular zone spleen pulp spleen trabecular artery spleen trabecular vein splenic cord splenic lymph node sputum stroma of pancreas subcapsular sinus floor subcapsular sinus of lymph node subparaventricular zone subsegmental bronchus superior frontal gyrus supraclavicular lymph node sympathetic ganglion sympathetic nerve systemic artery taste bud temporal lobe terminal bronchiole epithelium thoracic duct thoracic lymph node thymus thymus corticomedullary boundary thymus epithelium thymus subcapsular epithelium thymus trabecula tip of renal papilla tonsil tonsil germinal center trabecula of lymph node trabecular sinus of lymph node umbilical cord blood upper part of cisterna chyli venous blood venous blood vessel ventral pancreatic duct ventricular zone venule of lymph node visceral pleura white matter white matter of forebrain white pulp of spleen amygdala bed nucleus of stria terminalis brachial lymph node cerebellar nuclear complex cerebral cortex subventricular zone cerebral hemisphere cerebral nuclei cervical spinal cord claustrum of brain coronal suture corpus callosum cortex of kidney deep layer of superior colliculus dentate gyrus of hippocampal formation diencephalon dorsal horn of spinal cord dorsal lateral geniculate nucleus dorsal root ganglion dorsal tegmental nucleus dura mater endopeduncular nucleus globus pallidus hindbrain hypothalamic nucleus inguinal lymph node inner nuclear layer of retina lateral entopeduncular nucleus lateral hypothalamic area lateral zone of hypothalamus limbic system lumbar spinal cord lymphocyte domain medial amygdaloid nucleus meningeal cluster neurohypophysis nucleus accumbens olfactory bulb olfactory cortex olfactory epithelium paraventricular nucleus of hypothalamus primary visual cortex retrosplenial region rhomboidal nucleus sciatic nerve somatomotor area spinal nerve root striatum subfornical organ subiculum substantia nigra superior cervical ganglion telencephalon thalamic reticular nucleus utricle of membranous labyrinth ventral tegmental area ventricular system choroidal fissure ventromedial nucleus of hypothalamus visual cortex

Cell type T cell erythrocyte granulocyte mononuclear phagocyte natural killer cell platelet stem cell B cell endothelial cell epithelial cell monocyte plasmacytoid dendritic cell memory T cell plasma cell myeloid cell dendritic cell, human myeloid dendritic cell hematopoietic stem cell dendritic cell lymphocyte CD8-positive, alpha-beta T cell mast cell neutrophil promyelocyte megakaryocyte classical monocyte CD141-positive myeloid dendritic cell smooth muscle cell stromal cell CD1c-positive myeloid dendritic cell eosinophil macrophage non-classical monocyte conventional dendritic cell erythroid progenitor cell erythroblast erythroid lineage cell CD14-low, CD16-positive monocyte mature B cell memory B cell melanocyte CD4-positive, alpha-beta T cell neural cell CD14-positive monocyte common dendritic progenitor megakaryocyte-erythroid progenitor cell hematopoietic precursor cell mesenchymal stem cell metamyelocyte CD4-positive, alpha-beta memory T cell CD8-positive, alpha-beta memory T cell effector memory CD4-positive, alpha-beta T cell natural T-regulatory cell regulatory T cell alpha-beta T cell naive B cell effector CD4-positive, alpha-beta T cell naive thymus-derived CD4-positive, alpha-beta T cell naive thymus-derived CD8-positive, alpha-beta T cell hepatocyte CD4-positive, CD25-positive, alpha-beta regulatory T cell gamma-delta T cell activated CD4-positive, alpha-beta T cell plasmablast hematopoietic cell hematopoietic lineage restricted progenitor cell hematopoietic multipotent progenitor cell immature conventional dendritic cell CD16-positive, CD56-dim natural killer cell, human CD4-positive, alpha-beta cytotoxic T cell central memory CD8-positive, alpha-beta T cell effector T cell plasmacytoid dendritic cell, human transitional stage B cell type B pancreatic cell myelocyte T follicular helper cell CD4-negative, CD8-negative, alpha-beta intraepithelial T cell myofibroblast cell megakaryocyte progenitor cell mural cell T-helper 1 cell effector CD8-positive, alpha-beta T cell cytotoxic T cell effector memory CD8-positive, alpha-beta T cell effector memory CD8-positive, alpha-beta T cell, terminally differentiated mature CD8 single-positive thymocyte CD14-positive, CD16-positive monocyte basophil T-helper 17 cell T-helper 2 cell leukocyte memory regulatory T cell activated CD4-positive, alpha-beta T cell, human central memory CD4-positive, alpha-beta T cell naive T cell immature neutrophil mature neutrophil CD14-positive, CD16-low monocyte CD14-positive, CD16-negative classical monocyte granulocyte monocyte progenitor cell intermediate monocyte alternatively activated macrophage class switched memory B cell immature B cell pro-B cell regulatory B cell unswitched memory B cell Langerhans cell CD11b-positive dendritic cell monocyte-derived dendritic cell exhausted T cell B-1 B cell IgM memory B cell helper T cell adult endothelial progenitor cell progenitor cell reticulocyte CD4-positive helper T cell activated CD8-positive, alpha-beta T cell effector memory CD4-positive, alpha-beta T cell, terminally differentiated mature T cell CD16-negative, CD56-bright natural killer cell, human basophilic erythroblast inflammatory macrophage precursor B cell mucosa-associated lymphoid tissue macrophage naive regulatory T cell mesenchymal cell cycling T cell mucosal invariant T cell mature natural killer cell CD8-positive, alpha-beta cytotoxic T cell innate lymphoid cell pluripotent stem cell astrocyte glial cell orthochromatic erythroblast phagocyte blood cell endocrine cell neuron band form neutrophil cholangiocyte neutrophil progenitor cell neural stem cell myeloid suppressor cell immature basophil enucleate erythrocyte brain pericyte muscle cell osteoblast chondrocyte preosteoblast embryonic stem cell germinal center B cell myeloid lineage restricted progenitor cell microglial cell endodermal cell adipocyte neurogliaform cell lymphoid lineage restricted progenitor cell induced T-regulatory cell perivascular macrophage proerythroblast Schwann cell fibroblast mesodermal cell

ECs

SPs

Maximum number of markers to keep for each cell type

Start enrichment!

Download

CSV XLSX TSV

Plot celltype_ID

Save Ontology plot

PNG PDF

Click on a node to look at cell type description

Zoom: