is an Aggregator.
The Gene Expression Omnibus (GEO) is a public functional genomics data repository maintained by the NCBI at the U.S. National Library of Medicine. It archives and freely distributes high-throughput gene expression and other functional genomics datasets, including the single-cell and single-nucleus studies of human pancreatic islets that PanKbase identified and reprocessed.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| gene-expression-omnibus.portal | GEO Portal | geo | Graphical Interface | http | Web portal for searching, browsing, a... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| pankgraph.graph | PanKgraph Knowledge Graph | pankgraph.org | Graph | http | was influenced by | Pancreas-focused knowledge graph inte... |
| nde.graph | NIAID Data Ecosystem KG (graph) | nde | Graph | ttl | was influenced by | RDF (Turtle) knowledge graph of the N... |
| organoiddb.all-organoid-samples | OrganoidDB all organoid samples | all_org_samples (3.1 MB) | Product | csv | had primary source | Sample metadata for every organoid sa... |
| organoiddb.organoid-specificity-samples | OrganoidDB organoid specificity samples | org_specificity_samples (251.6 KB) | Product | csv | had primary source | Sample metadata for the organoid samp... |
| organoiddb.general-samples | OrganoidDB general samples | general_samples (91.8 KB) | Product | csv | had primary source | Sample metadata for the primary tissu... |
| klocd.portal | KLOCD Web Interface | www.organchip.cn | Graphical Interface | http | had primary source | KLOCD web interface for searching its... |
| omicsdi.portal | OmicsDI Portal | www.omicsdi.org | Graphical Interface | http | had primary source | Web portal for searching and browsing... |
| omicsdi.api | OmicsDI API | index.html | Programming Interface | http | had primary source | Swagger-documented web service for pr... |
| cfde-ddkg.archs4 | DDKG ARCHS4 Subgraph | ARCHS4.zip (10.8 MB) | Graph | csv | had primary source | Data Distillery ARCHS4 subgraph (buil... |
| sigcom-lincs.human-geo-signatures | Automatic Human GEO Signatures | human_geo_cd_sigs.tsv (2.0 GB) | Product | tsv | had primary source | Characteristic-direction gene express... |
| gtrd.downloads | GTRD Downloads | current | Product | http | was derived from | GTRD bulk download directory with pla... |
| gtrd.chip-seq_peaks | GTRD ChIP-seq Peaks | chip-seq | Product | http | was derived from | Per-species archives of transcription... |
| archs4.human.gene_counts | ARCHS4 Human Gene Counts | human_gene_v2.latest.h5 (57.6 GB) | Product | hdf5 | had primary source | Latest human gene-level ARCHS4 expres... |
| archs4.mouse.gene_counts | ARCHS4 Mouse Gene Counts | mouse_gene_v2.latest.h5 (45.7 GB) | Product | hdf5 | had primary source | Latest mouse gene-level ARCHS4 expres... |
| archs4.human.transcript_counts | ARCHS4 Human Transcript Counts | human_transcript_v2.latest.h5 (178.8 GB) | Product | hdf5 | had primary source | Latest human transcript-level ARCHS4 ... |
| archs4.mouse.transcript_counts | ARCHS4 Mouse Transcript Counts | mouse_transcript_v2.latest.h5 (105.8 GB) | Product | hdf5 | had primary source | Latest mouse transcript-level ARCHS4 ... |
| archs4.zoo | ARCHS4 Zoo Downloads | zoo | Product | hdf5 | had primary source | Collection page for ARCHS4 Zoo downlo... |
| chea-kg.graph | ChEA-KG Database | ❔ | Graph | neo4j | had primary source | Neo4j knowledge graph integrating tra... |
| chea-kg.libraries | ChEA-KG Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
| chea.libraries | ChEA Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
| genemania.networks | GeneMANIA Interaction Network Archive | current | Graph | txt | was derived from | Downloadable GeneMANIA interaction ne... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | Graph | neo4j | was derived from | Neo4j knowledge graph serialization o... |
| string.protein.links | STRING Protein Links | protein.links.v12.0.txt.gz (128.7 GB) | Graph | txt | had primary source | protein network data (full network, s... |
| string.protein.links.detailed | STRING Protein Links Detailed | protein.links.detailed.v12.0.txt.gz (189.6 GB) | Graph | txt | had primary source | protein network data (full network, i... |
| string.protein.links.full | STRING Protein Links Full | protein.links.full.v12.0.txt.gz (199.6 GB) | Graph | txt | had primary source | protein network data (full network, i... |
| string.protein.physical.links | STRING Protein Physical Links | protein.physical.links.v12.0.txt.gz (11.1 GB) | Graph | txt | had primary source | protein network data (physical subnet... |
| string.protein.physical.links.detailed | STRING Protein Physical Links Detailed | protein.physical.links.detailed.v12.0.txt.gz (13.8 GB) | Graph | txt | had primary source | protein network data (physical subnet... |
| string.protein.physical.links.full | STRING Protein Physical Links Full | protein.physical.links.full.v12.0.txt.gz (14.5 GB) | Graph | txt | had primary source | protein network data (physical subnet... |
| string.cog.links | STRING COG Links | COG.links.v12.0.txt.gz (176.8 MB) | Graph | txt | had primary source | association scores between orthologou... |
| string.cog.links.detailed | STRING COG Links Detailed | COG.links.detailed.v12.0.txt.gz (238.7 MB) | Graph | txt | had primary source | association scores (incl. subscores p... |
| string.database | STRING Database Network Schema | network_schema.v12.0.sql.gz (262.2 GB) | Graph | postgres | had primary source | full database, part II: the networks ... |
Gene Expression Omnibus (GEO)
The Gene Expression Omnibus (GEO) is a public functional genomics data repository operated by the NCBI. PanKbase used systematic searches of GEO to identify islet single-cell and single-nucleus studies (including those using IIDP- and Prodo-supplied islets), which were then reprocessed through a harmonized pipeline. GEO therefore acts as an aggregating upstream influence on PanKbase and PanKgraph.
Created: July 01, 2026 | Last modified: September 23, 2026