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CFDE Workbench
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
FEATURED

Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets

Given RNA-seq samples from a patient tumor, we screen for targets which are highly expressed in the tumor but lowly expressed across all healthy human tissues in GTEx. Detailed information about the selected target are queried from several DCCs.
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Mild Cognitive Impairment Use Case
FEATURED

Mild Cognitive Impairment Use Case

Find all IDG and GTEx assertions that may be related to mild cognitive impairment and any tissue type.
Mild Cognitive Impairment Use Case
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
FEATURED

Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets

Given RNA-seq samples from a patient tumor, we screen for targets which are highly expressed in the tumor but lowly expressed across all healthy human tissues in GTEx. Detailed information about the selected target are queried from several DCCs.
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Mild Cognitive Impairment Use Case
FEATURED

Mild Cognitive Impairment Use Case

Find all IDG and GTEx assertions that may be related to mild cognitive impairment and any tissue type.
Mild Cognitive Impairment Use Case
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
FEATURED

Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets

Given RNA-seq samples from a patient tumor, we screen for targets which are highly expressed in the tumor but lowly expressed across all healthy human tissues in GTEx. Detailed information about the selected target are queried from several DCCs.
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Mild Cognitive Impairment Use Case
FEATURED

Mild Cognitive Impairment Use Case

Find all IDG and GTEx assertions that may be related to mild cognitive impairment and any tissue type.
Mild Cognitive Impairment Use Case

All Use Cases

Explore different use cases that utilizes data from different CFDE participating programs
gene (9)
cancer (2)
small molecule (2)
exRNA (2)
variant (1)
pathway (1)
tissue (1)
disease (1)
protein (1)
Associations between Two Variants
Playbook Workflow Builder

Associations between Two Variants

Given two variants, we find their closest genes and present combined knowledge about them including their expression in tumors & healthy tissue, interactions between the two proteins, and gene sets containing the two genes.
Associations between Two Variants
variant
gene
cancer
CFDE Knowledge about a Gene
Playbook Workflow Builder

CFDE Knowledge about a Gene

We query several CFDE data sources for information about the gene provided.
CFDE Knowledge about a Gene
gene
Small Molecules to Induce a Biological Process
Playbook Workflow Builder

Small Molecules to Induce a Biological Process

We identify genes associated with a biological process from human, mouse phenotypes, KEGG pathways and GO gene set libraries. We then find Consensus LINCS compounds that upregulate these genes for inducing the biological process.
Small Molecules to Induce a Biological Process
gene
pathway
small molecule
Breast Epithelium Use Case
Data Distillery Knowledge Graph

Breast Epithelium Use Case

Find the genes that are highly expressed in breast epithelium as well as drugs that target these genes.
Breast Epithelium Use Case
gene
tissue
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Playbook Workflow Builder

Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets

Given RNA-seq samples from a patient tumor, we screen for targets which are highly expressed in the tumor but lowly expressed across all healthy human tissues in GTEx. Detailed information about the the selected target are queried from several DCCs.
Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
gene
cancer
CES1 Use Case
Data Distillery Knowledge Graph

CES1 Use Case

Display drugs that up or down regulate the gene CES1 from LINCS as well as tissues where it is highly expressed based on assertions from GTEx.
CES1 Use Case
gene
small molecule
Liquid Biopsy of Condition
Data Distillery Knowledge Graph

Liquid Biopsy of Condition

For a given set of genes that are highly expressed in a specific disease, identify extracellular RNAs (exRNAs) that may be detected in human biofluids and thus serve as non-invasive disease biomarkers.
Liquid Biopsy of Condition
exRNA
gene
disease
Frontotemporal Dementia Use Case
Data Distillery Knowledge Graph

Frontotemporal Dementia Use Case

For genes that are correlated with frontotemporal dementia, identify extracellular RNAs (exRNAs) that may be detected in human biofluids and thus serve as non-invasive disease biomarkers.
Frontotemporal Dementia Use Case
exRNA
gene
Related Proteins/Metabolites across DCCs
Playbook Workflow Builder

Related Proteins/Metabolites across DCCs

Using directly related proteins to a gene of interest, we return a slew of related information to the gene protein network from different DCCs.
Related Proteins/Metabolites across DCCs
gene
protein
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@CFDE Workbench 2026
The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
Consortium
About the CFDECF ProgramsCFDE CentersPartnershipsPilot Projects
Community
Workbench TutorialTraining & OutreachDocumentationGet QR CodesFunding Opportunities
Resources
Data & MetadataToolsChatbotUse CasesPublications
CFDE Workbench
Report a bug
The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
@CFDE Workbench 2026
This repository is under review for potential modification in compliance with Administration directives.