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Harmonizome specifications


Unique identifier OMICS_12543
Name Harmonizome
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Avi Ma’ayan

Publication for Harmonizome

Harmonizome citations


Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart

PMCID: 5948854
PMID: 29753320
DOI: 10.1186/s12933-018-0713-0

[…] I (http://www.informatics.jax.org) was used. Enrichment analysis was performed using g:GOST Gene Group Functional Profiling; g:Profiler (http://biit.cs.ut.ee/gprofiler/). Manual literature search and Harmonizome database [] were used to identify direct HIF-1 targets and predicted HIF-1 target genes, respectively. […]


Clustergrammer, a web based heatmap visualization and analysis tool for high dimensional biological data

Sci Data
PMCID: 5634325
PMID: 28994825
DOI: 10.1038/sdata.2017.151

[…] each gene, Clustergrammer automatically displays the full name and description of a gene as a tooltip when a user moves the mouse over a gene name. Gene full name and description are obtained via the Harmonizome API and reflect the most up to date version of this information. Another common function when exploring clusters from transcriptomics and proteomics studies is gene set enrichment analysis […]


Identification of high confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites

Genome Biol
PMCID: 5591525
PMID: 28886744
DOI: 10.1186/s13059-017-1298-8

[…] ting 5′ terminal oligopyrimidine (TOP) for mRNA translation []. HNRNPUL1 and NPM1 in group 4 (K562 cell line) were found to be supported by the Pathway Commons Protein-Protein Interactions dataset in Harmonizome database []. We also compared the RBP groups between these two cell lines (Additional file : Figure S10). A large proportion (17/21) of the shared RBPs were grouped with the other RBPs uni […]


Chronic Inhibition of STAT3/STAT5 in Treatment Resistant Human Breast Cancer Cell Subtypes: Convergence on the ROS/SUMO Pathway and Its Effects on xCT Expression and System xc Activity

PLoS One
PMCID: 4981357
PMID: 27513743
DOI: 10.1371/journal.pone.0161202

[…] P-seq, and other transcription factor binding site profiling studies assembled through the Ma'ayan Laboratory of Computational Systems Biology on-line database, Harmonizome (http://amp.pharm.mssm.edu/Harmonizome/dataset/CHEA+Transcription+Factor+Targets) [], microarray studies indicate a link between STATs and changes in xCT mRNA levels [,], and PathwayNet predicts a transcriptional connection bet […]

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Harmonizome institution(s)
Department of Pharmacology and Systems Therapeutics, Department of Genetics and Genomic Sciences, BD2K-LINCS Data Coordination and Integration Center (DCIC), Mount Sinai’s Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY, USA
Harmonizome funding source(s)
This work was supported from the national institutes of health (NIH) (R01GM098316, U54HL127624 and U54CA189201).

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