7. IXE-psoriasis-repressed ChIP-Seq node HCT intersection network

OVERVIEW
This network computes the extent and significance of intersections between (i) IXE-psoriasis-repressed (FC<0.66) confidence transcriptional targets (CTs) and (ii) high confidence transcriptional targets (HCTs) computed from ChIP-Seq consensomes for a set of signaling pathway nodes. IRCTS are defined as genes with an IXE-psoriasis consensome mean fold change <0.66 and a IXE psoriasis consensome q-value (FDR-corrected p-value) <0.05. Please refer to the IXE-psoriasis consensome for additional details.

METHODS
IRCTs were computed against HCTs derived from ChIP-Seq consensomes for a range of pathway nodes using the GeneOverlap package implemented in R. Intersections between IRCTs and node ChIP-Seq HCTs were assigned an FDR-corrected p-value (Q-VALUE), which corresponds to the probability that the intersection size is due to a random event.

INTERPRETATION
Cellular signaling pathway nodes (circles) in this network are organized according to SPP’s signaling pathway node-centric classification, which classifies nodes as receptors, enzymes, transcription factors, ion channels or co-nodes. Nodes are colored according to the category they belong to: orange = receptors; blue = enzymes; green = transcription factors; mustard = ion channels; grey = co-nodes. Nodes are grouped into functional classes in each category (rectangles). Node sizes are proportional to the -LOG10 of the intersection q-value: the larger the node the lower the q-value and the greater the confidence of the intersection between that node’s HCTs and IRCTs. Clicking a node will pull up a pane showing details on the data point, including the number of genes in the intersection of its HCTs and IRCTs.

FURTHER READING
To learn more about consensome analysis please refer to:
1. Ochsner et al. (2019) Sci Data 6, 252 10.1038/s41597-019-0193-4
2. Ochsner et al. (2021) Sci Data 7, 314 10.1038/s41597-020-00628-6
3. Bissig-Choisat et al. (2021) JHEP Reports 3, 100281 10.1016/j.jhepr.2021.100281
To learn more about HCT intersection analysis please refer to:
1. Ochsner et al. (2021) Sci Data 7, 314 10.1038/s41597-020-00628-6
2. Bissig-Choisat et al. (2021) JHEP Reports 3, 100281 10.1016/j.jhepr.2021.100281
3. Zapata et al. (2021) Transl Psychiatry 11, 405. 10.1038/s41398-021-01528-y