More - Kan-E/RNAseqChef GitHub Wiki

Volcano navi

Volcano navi shows volcano plot. The input format is as follows.

- The first column is gene name.
- A file includes columns named "log2FoldChange" and "padj".
- Other columns do not affect the analysis.

You can use not only RNA-seq data but also other omics data. By selecting genes from the GOI list, only the GOI can be labeled among the points displayed in the volcano plot. The x- and y-axis ranges could be freely changed by operating the slide bar. When the normalized count data are uploaded, the heatmap and boxplot of the genes selected from the GOI list are displayed.

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MSigDB gene set

The gene sets registered with MSigDB (Molecular Signatures Data Base) can be downloaded in this section.

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DoRothEA regulon

DoRothEA (Discriminant Regulon Expression Analysis) allows you to browse the data of DoRothEA. By entering the gene name in "Target name for TF search" and "TF name for target search", bi-directional search of "transcription factor ⇄ target gene" is possible. Confidence The official page recommends data with reliable confidence A-C. Enrichment analysis using RNAseqChef uses data with confidence A-C to increase the accuracy of transcription factor prediction.