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|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.|
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- person_outline Alexey A. Dmitrie
Publication for CrossHub
HK3 overexpression associated with epithelial mesenchymal transition in colorectal cancer
[…] [–]. 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
[…] 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
[…] 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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