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PATHFX RESULTS README
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Mike, thank you for using PathFX!

User:        Mike Wong <mikewong@sfsu.edu>
Analysis:    PathFX Example: Metformin
Description: Exploring phenotypes associated with Metformin
Drug:        Metformin
Targets:     [ none specified ]
Started:     Tuesday, Mar 26, 2019 at 10:31PM GMT
Version:     PathFX v1.0 beta

Included along with this file are your results. Please read the rest of this
file for a helpful guide to interpret your results.

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Result Files Descriptions
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In the zipped folder you receive, you will find the following files:

- One or more files with the ending neighborhood.txt: These are the protein
  neighborhoods for the individual drug targets.

- One or more files with the ending specific_neighborhood.txt: These are the
  protein neighborhoods after controlling for study bias in the interaction
  network. For further information, please see the website.

- The file ending with merged_neighborhood.txt: This is the full drug network
  after controlling for study bias and considering interactions from all drug
  targets. The edge scores between proteins and gene variants reflect the 
  amount and quality of evidence supporting the interaction. This edge score 
  is explained in [1] Wilson et al, 2018

- The file ending with merged_neighborhood__assoc_table.txt: This is a table of
  phenotypes associated with the network.

- The file ending with merged_neighborhood__assoc_database_sources.txt: This
  file lists where all gene-to-phenotype associations originate.

- The *.pkl files, including: lin_pandas_matrix.pkl,
  disease_clusters_lin_1.7.pkl, merged_neighborhood__cui_list_.pkl: These are
  intermediate files from the phenotype clustering phase of the algorithm.

- The cluster_membership_*.txt files: These are tables of phenotype clusters
  and the phenotypes assigned to each cluster.

- Two .png figures showing the results of the phenotype clustering: one file
  ending with labeledClusters_dendogram_full_1.7.png where the dendrogram
  labels show the top words associated with a particular cluster and one file
  ending with unlabeled_dendogram_full_1.7.png where the dendrogram labels show
  the number of phenotypes collapsed into a cluster or in the case of
  single-phenotypes clusters, the label shows the individual concept unique
  identifier (CUI).

- A file ending with merged_neighborhood__withDrugTargsAndPhens.txt: This is
  the complete protein network with phenotype interactions that is used for
  creating Cytoscape visualizations. The edge scores in this file are set to
  1.0 for all drug-to-protein interactions and gene-to-phenotype interactions.
  The edge scores between proteins and gene variants reflect the amount and
  quality of evidence supporting the interaction. This edge score is explained 
  in [1] Wilson et al, 2018.

- A file ending with network_nodeType.txt: This file specifies the entity type
  in the network file. It is also used with Cytoscape for visualization of the
  network.

- An optional file ending with graph.json: This file contains CytoscapeJS
  network visualization information created by using the Visualize Network
  function in this web application.

- This README.txt file explaining the data in the folder and containing details
  of the analysis and PathFX version information (for reproducibility).

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Citation
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[1] Wilson JL, Racz R, Liu T, Adeniyi O, Sun J, Ramamoorthy A, et al. (2018) PathFX
    provides mechanistic insights into drug efficacy and safety for regulatory
    review and therapeutic development. PLoS Comput Biol 14(12): e1006614.

    https://doi.org/10.1371/journal.pcbi.1006614


==============================================================================
PATHFX LOG
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SOURCE=.
ACTIVATE=/home/ubuntu/anaconda3/bin/activate
CONDA=/home/ubuntu/anaconda3/bin/conda
ENV=/home/ubuntu/.conda/envs/pathfx

cd /usr/local/pathfx/app/scripts && . /home/ubuntu/anaconda3/bin/activate /home/ubuntu/.conda/envs/pathfx && python phenotype_enrichment_pathway.py -d 'Metformin' -a '/usr/local/pathfx/app/results/users/a8214871/253'
gathering network data
calculating hypergeometric probabilities
saving to output


RUNNING PATHFX


PathFX added 5 targets from Drugbank

Metformin
results in: /usr/local/pathfx/app/results/users/a8214871/253/Metformin
full target list: SLC22A1 SLC47A1 PRKAB1 SLC22A3 SLC22A2
for analysis (targets within the interactome): SLC22A1 SLC47A1 PRKAB1 SLC22A3 SLC22A2
merging
starting phenotypic enrichment
creating files for visualization
