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###  FILE INFORMATION - clusterProfiler Results  ###
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Author:		Hannes Reinwald
Contact:	hannes.reinwald@ime.fraunhofer.de
Date:		14.04.2021
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We have conducted semi-static exposure studies with six neuronal targeting insecticides on 
fertilized zebrafish (Danio rerio) eggs, similar to the OECD 236 guideline for the 96h 
zebrafish embryo toxicity test. The aim for these transcriptomic profiling experiments was 
to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic 
vertebrate non-target model exposed to sub lethal concentrations of pesticides.


### GSEA ###

This directory contains the Gene Set Enrichment Analysis (GSEA) (Subramanian et al., 2005, DOI 10.1073/pnas.0506580102)
result tables performed on result tables from differential gene expression analysis (DGEA) with DESeq2.
To improve the signal to statistical noise ratio, obtained log2-fold change (lfc) values were shrunk 
with the apeglm method described by Zhu and colleagues (2019, DOI 10.1093/bioinformatics/bty895) before 
DGEA result tables were subjected to GSEA with via clusterProfiler (Yu et al., 2012, DOI 10.1089/omi.2011.0118) 
and reactomePA (Yu and He, 2016, DOI 10.1039/C5MB00663E).

For each tested substance and exposure condition a GSEA result table is provided for:
- KEGG pathways
- Reactome pathways
- Gene ontology

The corresponding R code is available under: 
https://github.com/hreinwal/zfeNeurotox

For experimental details please refer to our publication (Reinwald et al., 2021) or the accessible 
experiment description and treatment protocols deposited in the ArrayExpress database (www.ebi.ac.uk/arrayexpress).
The following ArrayExpress accession numbers provide access to the raw and 
DESeq2 normalized gene count matrices upon which these analysis were performed:

	Abamectin     -->  E-MTAB-9852
	Carbaryl      -->  E-MTAB-9855
	Chlorpyrifos  -->  E-MTAB-9853
	Fipronil      -->  E-MTAB-9854
	Imidacloprid  -->  E-MTAB-9859
	Methoxychlor  -->  E-MTAB-9860


###  DETAILED FILE INFO  ###

Each project folder (named after tested substance) contains a sub directory for
GO, KEGG pathway and Reactome pathway result tables called:
> gseGO
> gseKEGG
> gseReactome

For GSEA on GO we performed the analysis for biological process (BP), molecular function (MF) 
and cellular component (CC) separately. 

Further files are:

- multiGSEAres_[...].csv
  Merged GSEA result table for all tested substances only listing enriched
  terms with a padj < 0.05. Such a merged result table was generated for
  KEGG, Reactome and GO.BP results.

- SessionInfo_clusterProfiler.txt
  R session file created after completed data analysis, listing all used 
  packages including their currently applied version number.