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CrossHub specifications


Unique identifier OMICS_11688
Name CrossHub
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Users should download RNA-Seq, miRNA-Seq and methylation profiles (Illumina BeadChip) data from the TCGA Data Portal or other resources. CrossHub is released with dumps of ENCODE ChIP-Seq and Chromatin segmentation data, Jaspar matrix profiles and predictions, and five miRNA target databases. Otherwise, users can download source database files to parse them with CrossHub.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Alexey A. Dmitrie

Publication for CrossHub

CrossHub citations


HK3 overexpression associated with epithelial mesenchymal transition in colorectal cancer

BMC Genomics
PMCID: 5836836
PMID: 29504907
DOI: 10.1186/s12864-018-4477-4

[…] [–]. Recent studies showed that the glycolytic enzymes aldolase B (ALDOB), PKM2, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) play a role in EMT and metastasis in CRC [, ].In this work, using CrossHub software we analyzed RNA-Seq data from The Cancer Genome Atlas (TCGA) project to estimate the association between the expression of genes participating in EMT and glycolysis in CRC. Hexokinas […]


Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

BMC Genomics
PMCID: 5249009
PMID: 28105922
DOI: 10.1186/s12864-016-3351-5
call_split See protocol

[…] We analyzed TCGA RNA-Seq datasets (read counts) for colon cancer using CrossHub software []. Here is a brief description of TCGA RNA-Seq Version 2 pipeline. Illumina reads were aligned to hg19 UCSC reference genome using MapSplice []. The alignment results were translate […]


The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection

PMCID: 4940579
PMID: 27433286
DOI: 10.1155/2016/2353560

[…] uate the coexpression of human genes (p ≤ 0.001 was taken as the criterion of statistical significance). We supplemented the coexpression analysis with ENCODE ChIP-Seq data using previously developed CrossHub tool []. […]


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CrossHub institution(s)
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; N.N. Blokhin Russian Cancer Research Center, Moscow, Russia; Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia; M.M. Shemyakin-Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
CrossHub funding source(s)
The Russian Science Foundation grant no. 14-35-00107; the Russian Science Foundation grant no. 14-15-01083

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