is an Aggregator.
SigCom LINCS is a web search engine from the Ma'ayan Laboratory, built on the Signature Commons framework, that serves more than a million gene expression signatures processed from LINCS (mostly L1000 chemical, shRNA, CRISPR knockout, overexpression, and ligand perturbations), GTEx, and GEO. Users run rank-based signature similarity searches to find perturbations that mimic or reverse a query signature, and search metadata about signatures, datasets, genes, and drugs. All data are available through a metadata API, a data API, and bulk downloads.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| sigcom-lincs.portal | SigCom LINCS Web Application | sigcom-lincs | Graphical Interface | http | Web search engine for running signatu... |
| sigcom-lincs.metadata-api | SigCom LINCS Metadata API | metadata-api | Programming Interface | json | Signature Commons metadata API (LoopB... |
| sigcom-lincs.data-api | SigCom LINCS Data API | data-api | Programming Interface | json | Signature Commons data API (Enrichmen... |
| sigcom-lincs.documentation | SigCom LINCS Documentation | SigCom%20LINCS%20Documentation.ipynb (15.1 KB) | Documentation | http | Jupyter notebook tutorial documenting... |
| sigcom-lincs.cp-consensus | L1000 Chemical Perturbation Consensus Signatures | cp_mean_coeff_mat.tsv.gz (1.8 GB) | Product | tsv | Consensus (mean) characteristic-direc... |
| sigcom-lincs.xpr-consensus | L1000 CRISPR Knockout Consensus Signatures | xpr_mean_coeff_mat.tsv.gz (412.5 MB) | Product | tsv | Consensus (mean) characteristic-direc... |
| sigcom-lincs.cp-gmt | L1000 Chemical Perturbation Gene Sets | l1000_cp.gmt (2.1 GB) | Product | tsv | Up and down gene sets for each L1000 ... |
| sigcom-lincs.xpr-gmt | L1000 CRISPR Knockout Gene Sets | l1000_xpr.gmt (418.1 MB) | Product | tsv | Up and down gene sets for each L1000 ... |
| sigcom-lincs.shrna-gmt | L1000 shRNA Gene Sets | l1000_shRNA.gmt (478.4 MB) | Product | tsv | Up and down gene sets for each L1000 ... |
| sigcom-lincs.oe-gmt | L1000 Overexpression Gene Sets | l1000_oe.gmt (101.1 MB) | Product | tsv | Up and down gene sets for each L1000 ... |
| sigcom-lincs.cp-coefficients | L1000 Chemical Perturbation Signature Matrix | cp_coeff_mat.gctx (33.6 GB) | Product | hdf5 | Characteristic-direction coefficient ... |
| sigcom-lincs.drug-similarity | L1000 Drug-Drug Similarity Matrix | L1000_2021_cosine_drug_similarity_lm.h5 (4.2 GB) | Product | hdf5 | Drug-drug cosine similarity matrix co... |
| sigcom-lincs.gene-similarity | L1000 Gene-Gene Similarity Matrix | L1000_2021_cosine_gene_similarity_lm.h5 (215.3 MB) | Product | hdf5 | Gene-gene cosine similarity matrix co... |
| sigcom-lincs.small-molecules | LINCS Small Molecule Metadata | LINCS_small_molecules.tsv (3.8 MB) | Product | tsv | Metadata for the LINCS small molecule... |
| sigcom-lincs.human-geo-signatures | Automatic Human GEO Signatures | human_geo_cd_sigs.tsv (2.0 GB) | Product | tsv | Characteristic-direction gene express... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| reprotox-kg.graph.sigcom-lincs | ReproTox-KG SigCom LINCS Drug-Gene Graph | sigcom_lincs_serialization.valid.json (109.3 MB) | Graph | json | had primary source | Drug-to-gene up- and down-regulation ... |
SigCom LINCS is a gene expression signature search engine from the Ma’ayan Laboratory at the Icahn School of Medicine at Mount Sinai, built on the Signature Commons framework. As of October 2026 it indexes 1,113,059 signatures from 431 datasets. Most come from LINCS L1000 perturbations: chemical (718,055), shRNA (158,003), CRISPR knockout (140,945), overexpression (34,164), and ligand (7,546). Others come from GTEx and from automatically processed human and mouse GEO studies.
Users can search with up and down gene sets or a single gene set to rank signatures that mimic or reverse the query, and can search metadata for signatures, datasets, genes, and drugs. Everything in the web interface is also available through the Signature Commons metadata API and data API, both registered in SmartAPI. Bulk downloads include consensus and individual L1000 signature matrices, GMT gene sets for each perturbation type, drug-drug and gene-gene similarity matrices, small-molecule metadata, and automatic GEO signatures, along with mirrored CREEDS and CLUE files.
The site states no license for its data. It asks users to cite Evangelista et al. 2022 (Nucleic Acids Research). SigCom LINCS feeds the SigCom LINCS drug-gene graph in ReproTox-KG.
Created: October 10, 2026 | Last modified: October 10, 2026