The PathCellNet is a compendium of immunologically relevant context-specific gene-gene association networks inferred from genome-wide transcriptional profiles deposited in public repositories. The tool can be used to visualize context-specific network and design gene-centric gene-sets. The data-set across different platforms are used; normalization and filtering procedures are described in (Katanic et. al 2016).

To define the context, select pathogen using "Pathogen" tab and cell-type using "Cell Type" tab. Note that cell types analyzed depends on the availability of the respective data-sets in public domain. The cell-types with very few independent studies are not included. You can suggest a context using “Desired Context” tab on the main page.

The two types of networks can be visualized, i) Shortest Path tab will reveal the shortest paths between the genes provided in the gene-set, and ii) Nearest neighbor tab will provide the nearest neighbors of the genes provided by the users and connects the neighbors.


Influenza

Monocyte Derived Dendritic Cells (MDDCs)

The transcriptomic data from GSE41067 and GSE55278 studies were integrated. Briefly, these are time-course studies measuring gene-expression upon influenza infections until 8 hours post infection.

A549 Epithelial Cells

The transcriptomic data from GSE19580, GSE31469, GSE31470, GSE31471, GSE31472, GSE31473, GSE31474, GSE31518, and GSE47937 studies were integrated. Briefly, these are time-course studies measuring gene-expression upon influenza infections until 24 hours post infection.

Peripheral Blood Monocytes (PBMCs)

The transcriptomic data from GSE30550 and GSE52428 studies were integrated. Briefly, these are time-course studies measuring gene-expression upon influenza infections until 12 hours post infection.

Reference

Dejan Katanic, Atif Khan and Juilee Thakar, 2016. PathCellNet: cell-type specific pathogen-response network explorer, Journal of Immunological Methods, 439:15-22


Gene List

Common Network


Respiratory Syncytial Virus (RSV)

Peripheral Blood Monocytes (PBMCs)

The transcriptomic data from GSE34205 and GSE69606 studies focusing on pediatric population were integrated. Briefly, GSE34205 study includes healthy controls and RSV infected subjects, and GSE69606 study includes mild, moderate and severe RSV infected subjects along with recovered time points.

Reference:

Manuscript in preparation