PathON - Pathway Analysis Tool

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With PathON, starting from RNAseq data, you can:

What core components of a signaling pathway are up-regulated under experimental conditions?
What transcription factor targets of a signaling pathway are up-regulated under experimental conditions?
Your input: RNAseq data (FPKM values) for control and experimental samples
A

control conditions
(1 or more replicate)
B

experimental conditions,
e.g. +drug, time, etc.
(1 or more replicate)
PathON will
  1. Average replicates
  2. Compute B/A ratio
  3. Select hits based on a user-defined threshold
  4. Compare hits to pathway
PathON will provide
List of pathways annotated with
  • genes enriched in B vs. A
  • P-value for pathway enrichment
  • network view
  • heat map of expression

A

1 condition
(1 or more replicate)
PathON will
  1. Average replicates
  2. Compute a ratio based on the average
  3. Select hits based on a user-defined threshold
  4. Compare hits to pathway
PathON will provide
List of pathways annotated with
    List of pathways annotated with
  • genes enriched in B vs. A
  • P-value for pathway enrichment
  • network view
  • heat map of expression


Your input: Pre-computed ratio for 2 conditions

control conditions
(1 or more replicate)
PathON will
  1. Select hits based on a user-defined threshold
  2. Compare hits to pathway
PathON will provide
List of pathways annotated with
  • genes enriched in B vs. A
  • P-value for pathway enrichment
  • network view
  • heat map of expression


Your input: RNAseq data (FPKM values) for control and experimental samples
A

hit list
B

background list
(list of what was tested)
PathON will
  1. Compare hits to pathway, using background list to compute enrichment
Your input: a ‘hit list’ and a ‘background list’
List of pathways annotated with
  • genes enriched in B vs. A
  • P-value for pathway enrichment
  • network view
  • heat map of expression


What ligand is sent by a source tissue (or cell type or organ)? What core components or transcription factor targets are up-regulated in the putative target/receiving tissue (or cell type or organ)?
Your input: RNAseq data (FPKM values) for control and experimental samples
A

hit list
B

“signal source” tissue or cell type, experimental (1 or more replicate)
C

“signal target” tissue or cell type, control (1 or more replicate)
D

“signal target” tissue or cell type, experimental (1 or more replicate)
PathON will
  1. Average replicates for the source and target
  2. Compute ratio for source (B/A) and target (D/C)
  3. Select hits based on a user-defined threshold
  4. Evaluate ligands (source)
  5. Compare hits to pathway information (target)
Your input: a ‘hit list’ and a ‘background list’
List of pathways annotated with
  • ligands present (source)
  • genes enriched in D vs. C
  • P-value
  • network view + heat map