---
title: "LINCS L1000 (Clue.io) API Reference"
description: "| 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 |"
type: skill
canonical_url: https://claudary.paisolsolutions.com/skills/lincs-l1000
source: "Claudary"
difficulty: intermediate
author: "Claude Code Knowledge Pack"
date: 2026-07-10T11:30:36.220Z
license: CC-BY-4.0
attribution: "LINCS L1000 (Clue.io) API Reference — Claudary (https://claudary.paisolsolutions.com/skills/lincs-l1000)"
---

# 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 |

## 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

```bash
# 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):
```json
[
  {
    "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

---

Source: [Claudary](https://claudary.paisolsolutions.com/skills/lincs-l1000) · https://claudary.paisolsolutions.com