PathON - Pathway Analysis Tool For Drosophila
With PathON, starting from RNAseq data, you can:
- detect up-regulation of core signaling components
- detect up-regulation of signal pathway target genes
- view enriched pathways (genes, networks, heat maps)
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)
control conditions
(1 or more replicate)
B
experimental conditions,
e.g. +drug, time, etc.
(1 or more replicate)
experimental conditions,
e.g. +drug, time, etc.
(1 or more replicate)
PathON will
- Average replicates
- Compute B/A ratio
- Select hits based on a user-defined threshold
- 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
A
1 condition
(1 or more replicate)
1 condition
(1 or more replicate)
PathON will
- Average replicates
- Compute a ratio based on the average
- Select hits based on a user-defined threshold
- Compare hits to pathway
PathON will provide
List of pathways annotated with
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)
control conditions
(1 or more replicate)
PathON will
- Select hits based on a user-defined threshold
- 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: RNAseq data (FPKM values) for control and experimental samples
A
hit list
hit list
B
background list
(list of what was tested)
background list
(list of what was tested)
PathON will
- Compare hits to pathway, using background list to compute enrichment
Your input: a ‘hit list’ and a ‘background list’
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
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
hit list
B
“signal source” tissue or cell type, experimental (1 or more replicate)
“signal source” tissue or cell type, experimental (1 or more replicate)
C
“signal target” tissue or cell type, control (1 or more replicate)
“signal target” tissue or cell type, control (1 or more replicate)
D
“signal target” tissue or cell type, experimental (1 or more replicate)
“signal target” tissue or cell type, experimental (1 or more replicate)
PathON will
- Average replicates for the source and target
- Compute ratio for source (B/A) and target (D/C)
- Select hits based on a user-defined threshold
- Evaluate ligands (source)
- Compare hits to pathway information (target)
Your input: a ‘hit list’ and a ‘background list’
List of pathways annotated with
List of pathways annotated with
- ligands present (source)
- genes enriched in D vs. C
- P-value
- network view + heat map