Skillintermediate

LINCS L1000 (Clue.io) API Reference

| Endpoint | Description | |---|---| | `GET /perts` | Query perturbagens (compounds, gene knockdowns, overexpression) | | `GET /genes` | Query genes (L1000 landmark + inferred) | | `GET /cells` | Query cell lines used in L1000 | | `GET /sigs` | Query connectivity signatures | | `GET /profiles` | Access expression profiles (level 5 z-scores) | | `GET /pcls` | Perturbagen classes |

Claude Code Knowledge Pack7/10/2026

Overview

LINCS L1000 (Clue.io) API Reference

Overview

The LINCS L1000 dataset is accessible via the Connectivity Map (CMap) API at clue.io.

Base URL

https://api.clue.io/api

Authentication

API key required (free registration at clue.io)
Pass via header: user_key: YOUR_API_KEY

Key Endpoints

Endpoint	Description
`GET /perts`	Query perturbagens (compounds, gene knockdowns, overexpression)
`GET /genes`	Query genes (L1000 landmark + inferred)
`GET /cells`	Query cell lines used in L1000
`GET /sigs`	Query connectivity signatures
`GET /profiles`	Access expression profiles (level 5 z-scores)
`GET /pcls`	Perturbagen classes

Query Parameters

All endpoints support a filter parameter using Loopback-style JSON:

where — filter conditions
fields — select specific fields
limit / skip — pagination

Example Calls

# Search for a compound perturbagen by name
curl -H "user_key: YOUR_API_KEY" \\
  "https://api.clue.io/api/perts?filter={\\"where\\":{\\"pert_iname\\":\\"vorinostat\\"}}"

# Get landmark genes
curl -H "user_key: YOUR_API_KEY" \\
  "https://api.clue.io/api/genes?filter={\\"where\\":{\\"is_lm\\":true},\\"limit\\":10}"

# Query cell lines
curl -H "user_key: YOUR_API_KEY" \\
  "https://api.clue.io/api/cells?filter={\\"where\\":{\\"cell_iname\\":\\"MCF7\\"}}"

# Get connectivity signatures for a compound
curl -H "user_key: YOUR_API_KEY" \\
  "https://api.clue.io/api/sigs?filter={\\"where\\":{\\"pert_iname\\":\\"vorinostat\\"},\\"limit\\":5}"

Response Format

JSON. Example (perturbagen):

[
  {
    "pert_id": "BRD-K81418486",
    "pert_iname": "vorinostat",
    "pert_type": "trt_cp",
    "moa": ["HDAC inhibitor"],
    "target": ["HDAC1","HDAC2","HDAC3","HDAC6"]
  }
]

Rate Limits

Free tier: moderate rate limiting (exact numbers not publicly documented)
Bulk data downloads available separately via clue.io data portal