Shiny R web-app for comparing perturbed pathways associated to different phenotypes.
URL: https://alpha.dmi.unict.it/shiny/users/gmicale/PathwayComparator/.
Input data:
Three types of text files can be uploaded by the user for pathway comparison:
- Custom file
- MITHrIL perturbation file
- PHENSIM simulation file
Example files are available in the "Data" folder.
Currently supported organisms:
- Human
- Mouse
- Rat
More organisms will be supported in the future.
Custom file:
The user can provide the app with any custom text file containing a score for each biological element. The first line of the text file must contain the common name of one of the supported organisms (e.g. 'Human', 'Mouse') to which biological elements belong. The following lines indicate for each biological entity (gene, miRNAs, compound) a perturbation score. Nodes are referred to by the id of the corresponding biological element, which must be:
- The Entrez ID for genes
- The miRBase entry name for miRNAs
- The ChEBI id, the KEGG COMPOUND id or the KEGG GLYCAN id for chemical compounds
- The KEGG DRUG id for drugs Perturbation score can be any real number (positive, negative or zero).
Example:
Human 6197 -3.74 6196 0 hsa-miR-199b-3p 0 hsa-miR-128-3p 2.5 hsa-miR-214-3p 0 chebi:43474 0
MITHrIL perturbation file:
MITHrIL evaluate the de-regulation of pathways due to expression changes of one or more pathway elements. MITHrIL requires a list of biological entities with their log-fold expression changes as input. De-regulation of pathway nodes is measured by a perturbation score, which can be positive or negative. MITHril is available as a command line tool (https://github.com/alaimos/mithril-standalone), and its output is a perturbation file that can be directly uploaded as input to PACO. The scores associated with nodes and used by PACO are the values of the "Perturbation" column.
Example:
# Pathway Id Pathway Name Gene Id Gene Name Perturbation Accumulator pValue path:hsa00190 Oxidative phosphorylation - Enriched 64077 LHPP 0.45 1.36 1.0 path:hsa00190 Oxidative phosphorylation - Enriched 5464 PPA1 2.10 3.56 1.0 path:hsa00190 Oxidative phosphorylation - Enriched hsa-miR-101-3p hsa-miR-101-3p -0.79 -2.45 1.0
PHENSIM simulation file:
PHENSIM (PHENotype SIMulator) (https://phensim.tech/) is a tool developed to simulate the de-regulation of pathways biological elements, as a result of the over- or under-expression of user-specified molecules (e.g. genes or miRNAs). De-regulation of pathway nodes is measured by an activity score, which can be positive or negative, denoting a biological element which is more or less active than normal condition. Scores associated to nodes are the values of "Activity Score" column.
Example:
# Pathway Id Pathway Name Node Id Node Name Is Endpoint Is Direct Target Activity Score P-Value Adjusted P-Value Log-Probabilities (Activation, Inhibition, Others) Pathway Activity Score Pathway p-value Pathway Adjusted p-value Pathway Log-Probabilities (Activation, Inhibition, Others) Direct Targets Average Node Perturbation Average Pathway Perturbation R-HSA-198753 ERK/MAPK targets 6197 RPS6KA3 Yes No 0.0 0.9980000000000008 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 0.0 0.5760000000000004 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 0.0 -2.4006391023997053E-5 R-HSA-198753 ERK/MAPK targets 6196 RPS6KA2 No No 0.0 0.9960000000000008 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 0.0 0.5760000000000004 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 0.0 -2.4006391023997053E-5 R-HSA-198753 ERK/MAPK targets hsa-miR-199b-3p hsa-miR-199b-3p No No 0.0 0.9970000000000008 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 0.0 0.5760000000000004 1.0 -20.72326583994641,-20.72326583994641,-1.999999945436137E-9 -6.314636151692764E-13 -2.4006391023997053E-5
Example of usage:
We want to compare perturbed immune system pathways (specifically the "Interferon Signaling" pathway) in mice and humans, following the upregulation of Interferon (IFN)-stimulated gene 15 (ISG15), a ubiquitin-like protein that functions both as an extracellular cytokine and an intracellular protein modifier.
As a preliminary step, we first run two simulations using PHENSIM by upregulating ISG15 in humans and mice, respectively.
Connect to the PHENSIM web portal1. Click on "Simulations" on the left sidebar. From the simulation page that appears, clik on "New simple simulation".
Following the guided procedure, indicate a name for the new simulation and select "Homo sapiens" as organism. Next, write "ISG15" in the filter of "NAME" column and click on the red up-arrow to include ISG15 as up-regulated gene in the simulation. Finally, select the option "Add REACTOME pathways" in the "SELECT OPTIONAL PARAMETERS" tab to include REACTOME pathways in the simulation and click on "Create simulation" to run PHENSIM.
The launched simulation will then appear on the list of all simulations launched so far by the user using the PHENSIM portal, accessible by clicking on "Simulations" on the left sidebar. When the simulation ends, i.e. the value of the "STATUS" column in the table is "Completed", download the PHENSIM simulation file as follows:
- Go to the "Simulations" panel
- Click on "Show simulation" ('eye' icon on the right)
- Go to the "Download results" box at the bottom of the page and click "Download raw results."
To perform a PHENSIM simulation by upregulating ISG15 in mice, repeat the same steps on the PHENSIM portal, selecting now "Mus Musculus" as organism.
Next, upload the two files into PACO and click on the "Compare" button. In the visualization panel, choose "Interferon Signaling" as "Pathway" and (optionally) "ISG15" as "Gene" to focus only on ISG15 gene and on its direct neighbors in the "Interferon Signaling" pathway of human and mouse.
References:
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Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A (2016). Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. Oncotarget 7(34):54572-54582. https://doi.org/10.18632/oncotarget.9788
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Alaimo S, Rapicavoli RV, Marceca GP, La Ferlita A, Serebrennikova OB, et al. (2021). PHENSIM: Phenotype Simulator. PLOS Computational Biology 17(6): e1009069. https://doi.org/10.1371/journal.pcbi.1009069
Footnotes
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Before using PHENSIM web portal, a registration is required. After registration, log in to start new simulations. ↩