# The LINCS DCIC Engagement Plan with the CFDE

> **NIH NIH OT2** · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · 2024 · $300,000

## Abstract

Driving scientific questions that will be addressed by engaging with the CFDE and why it has not
yet been feasible
The Library of Integrated Network-based Cellular Signatures (LINCS) program (1) collected massive data
from human cells perturbed by thousands of single small molecules as well as knockouts, knockdowns,
and over-expression of single genes. The diverse collections of perturbed human cells (n>50) were profiled
before and after the perturbations with an array of omics assays that include transcriptomics, proteomics,
epigenomics, cell viability, and imaging at different time points and where the small molecules were applied
in different concentrations. Altogether, over 2 million signatures are expected to be produced and provided
as a resource for the community for query and reuse at the time when the LINCS program officially ends
(6/2020). Such a resource can be used for limitless applications, for example, to study molecular
mechanisms of disease, repurpose existing drugs, predict side effects and indications for pre-clinical small
molecules, associate small molecules with the targets that they likely affect directly and indirectly,
reconstruct cell signaling and gene regulatory networks, understand the global space of all possible cellular
states in response to all possible perturbations of all human cells, and many more applications and use
cases. This utilization of LINCS resources is already happening but can be significantly enhanced via
continued efforts led by the LINCS Data Coordination and Integration Center (DCIC) through interactions
with the CFDE and other CF DCCs in the next 3 years.
So far, the ~400 publications produced by the LINCS consortium have been cited by ~6,000 other papers,
demonstrating the high impact of the program on the research community. In particular, the computational
resources developed by the LINCS DCIC have been very successful. These tools and databases were
already visited by >1 million unique users, with currently ~30,000 unique users per month (based on Google
Analytics). These strong usage statistics demonstrate the value of LINCS resources and their potential for
making long-lasting impact on drug discovery, and the biomedical research community in general. The
LINCS DCIC developed web-based resources to enable the federated access, intuitive querying, and
integrative analysis and visualization of the LINCS data combined with other relevant data. To achieve this
the LINCS DCIC also processed many additional external data types from other relevant resources to be
integrated with LINCS data including data from other Common Fund programs such as GTEx, Epigenomics
Roadmap, and IMPC. However, such data integration efforts were achieved with little consideration of
community standards to ensure their long term findability, accessibility, interoperability and reusability
(FAIR) (2). Our involvement with the NIH Data Commons Pilot Project Consortium (DCPPC) and the
Common Fund Data Ecosystem (CFDE) tau...

## Key facts

- **NIH application ID:** 11089689
- **Project number:** 3OT2OD030160-01S5
- **Recipient organization:** ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
- **Principal Investigator:** Avi Ma'ayan
- **Activity code:** OT2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $300,000
- **Award type:** 3
- **Project period:** 2020-09-23 → 2025-09-22

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11089689

## Citation

> US National Institutes of Health, RePORTER application 11089689, The LINCS DCIC Engagement Plan with the CFDE (3OT2OD030160-01S5). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/11089689. Licensed CC0.

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