RNA-seq data analysis in Genome Enhancer


RNA-seq data analysis in Genome Enhancer

Genome Enhancer is a fully automatized pipeline for analysing patient omics data and studying the molecular mechanism underlying the observed pathology. Genome Enhancer identifies prospective drug targets and associated treatments from the input omics data, supported data formats include RNA-seq transcriptomics data.


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We provide a number of demo reports demonstrating how Genome Enhancer results would look like on various inputs. Full list of all available demo reports can be found here. Below you will find two demo reports demonstrating how analysis results of raw FASTQ files and pre-processed table with LogFC values would look like in Genome Enhancer.


Demo report ‘Esophageal Squamous Cell Carcinoma (GSE32424) — Transcriptomics, FASTQ’ – demonstrating how raw RNA-seq FASTQ data can be analysed in Genome Enhancer:


Demo report ‘Parkinson disease, induced a-Syn expression in SH-SY5Y cells (GSE145804) — Transcriptomics, LogFC Table’ – demonstrating how pre-processed RNA-seq data in the format of table with calculated LogFC values can be analysed in Genome Enhancer:
Other demo reports, which also include combinations of transcriptomics data with other omics data types, can be found here.


How does it work


Genome Enhancer uses Upstream Analysis, an integrated promoter and pathway analysis, to identify potential drug targets of the studied pathology.

In the first step of this analysis the transcription factors that regulate differentially expressed genes are identified with the use of the TRANSFAC® database of transcription factors binding sites.

The second step searches for common master-regulators of the identified transcription factors by building a personalized signal transduction network of the studied pathology using the TRANSPATH®   database of  mammalian signal transduction and

metabolic pathways. The identified master regulators are prospective drug target candidates. They are used for further selection of chemical compounds that can bring therapeutic benefit for the studied clinical case. In this step the HumanPSD database is employed to identify drugs that have been tested in clinical trials. The cheminformatic tool PASS predicts small molecules that can affect the identified targets.

Finally, Genome Enhancer generates a comprehensive analysis report about the personalized drug targets identified for a certain patient, or a group of patients, and the drugs that may be effective in this case. You can view a number of Genome Enhancer demo reports here.


A detailed description of full Genome Enhancer analysis schema, including all steps of RNA-seq data pre-processing, which are performed by the system for finding the differentially expressed genes, can be found on this page. Transcriptomics data can be loaded to Genome Enhancer in one of the following formats:

    • Table data
    • FASTQ files
    • Affimetrix files
    • Agilent files
    • Illumina files

You are welcome to purchase a paid subscription for Genome Enhancer by requesting it here.

For further info please explore the Genome Enhancer product page.

For any questions please feel free to contact us via info@genexplain.com