Here, we surveyed bioinformatics software tools for exploring gene expression connectivity mapping. Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Connectivity mapping is a…
Web app
iATC-mISF iATC-mISF

iATC-mISF

A web-server used to identify Anatomical Therapeutic Chemical (ATC) class.…

A web-server used to identify Anatomical Therapeutic Chemical (ATC) class. iATC-mISF was developed by incorporating the information of chemical-chemical interaction, the information of the structural…

C2Maps C2Maps

C2Maps

An online bioinformatics resource that provides biologists with directional…

An online bioinformatics resource that provides biologists with directional relationships between drugs and genes/proteins in specific disease contexts based on network mining, literature mining, and…

Drug directionality… Drug directionality Map

DMAP Drug directionality Map

An in silico drug-protein connectivity map, which contains directed…

An in silico drug-protein connectivity map, which contains directed drug-to-protein effects and effect scores. DMAP that can help drug development researchers evaluate what effects a drug may have on…

Desktop app
Probabilistic… Probabilistic connectivity mapping

ProbCMap Probabilistic connectivity mapping

A probabilistic drug connectivity mapping method that can be used to infer drug…

A probabilistic drug connectivity mapping method that can be used to infer drug similarities based on drug treatment gene expression measurements from multiple cell lines, such as the Connectivity…

Desktop app
Co-expressed gene-set… Co-expressed gene-set enrichment analysis

Cogena Co-expressed gene-set enrichment analysis

A fully configurable framework for co-expressed gene set enrichment analysis.…

A fully configurable framework for co-expressed gene set enrichment analysis. By combining pathway analysis and drug repositioning analysis, Cogena provides a unique approach to imply the drug mode…

The LincsCloud… The LincsCloud Connectivity Map

The LincsCloud Connectivity Map

A large-scale pharmacogenomics dataset to link disease-associated…

A large-scale pharmacogenomics dataset to link disease-associated transcriptional signatures with chemical and genetic perturbagen-associated transcriptional signatures. Lincscloud is designed to…

Desktop app
QUB Accelerated Drug… QUB Accelerated Drug And Transcriptomic…

QUADrATiC QUB Accelerated Drug And Transcriptomic Connectivity

A user-friendly tool for the exploration of gene expression connectivity on the…

A user-friendly tool for the exploration of gene expression connectivity on the subset of the library of integrated cellular signatures data set corresponding to FDA-approved small molecule…

Desktop app
statistically… statistically significant connections' map

sscMap statistically significant connections' map

A Java application designed to undertake connectivity mapping tasks. sscMap is…

A Java application designed to undertake connectivity mapping tasks. sscMap is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from…

Web app
Gene-Set Local… Gene-Set Local Hierarchical Clustering

GSLHC Gene-Set Local Hierarchical Clustering

A platform which is based on a GSA-based version of CMap, Gene-Set Connectivity…

A platform which is based on a GSA-based version of CMap, Gene-Set Connectivity Map (GSCMap), in which all the genomic profiles in CMap are converted, using gene-sets from the Molecular Signatures…

Web app
A A A Connectivity Map Connectivity Map

cmap Connectivity Map

A reference collection of gene-expression profiles from cultured human cells…

A reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. CMAP resource can be…

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