example analysis refined

Author: hosseinvk

04-example-dataset.Rmd

@@ -8,27 +8,30 @@ With appropriate treatment, it can be induced to differentiate into a ‘more ne
 Differentiated cells look quite different, growing thin neurites out from the body of the cell.
 
 
-![SH-SY5Y](https://monashbioinformaticsplatform.github.io/enrichment_analysis_workshop/img/shsy5ydiff.png)
+<!-- ![SH-SY5Y](https://monashbioinformaticsplatform.github.io/enrichment_analysis_workshop/img/shsy5ydiff.png) -->
 <!-- seems to point to content dir not common root : ![shsy5](/img/shsy5ydiff.png)-->
 
-_Image is derived from Figure 4 (Pezzini et al. 2017)_
 
+```{r, echo=FALSE, out.width="100%", fig.align = "center", fig.cap="Morphological analysis of differentiated SH-SY5Y cells.<br>At 6-DIV stage, the cells exposed to RA showed an elongated morphology as compared to basal medium (NT). Cells subsequently treated in NBM for 3 days became more polarised, exhibited several neurites and branches and acquired a neuronal-like shape<br><br>Image is derived from Figure 4 (Pezzini et al. 2017)."} 
+#knitr::include_graphics("https://monashbioinformaticsplatform.github.io/enrichment_analysis_workshop/img/shsy5ydiff.png")
+knitr::include_graphics("images/shsy5ydiff.png")
+```
 
+<!-- _Image is derived from Figure 4 (Pezzini et al. 2017)_ -->
 
-## The question: What pathways are involved in SH-SY5Y Differentiation?
 
-In their paper [_Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells_](https://link.springer.com/article/10.1007%2Fs10571-016-0403-y) Pezzini et al induced differentiation of the SH-SY5Y Neuroblastoma cell line and measured transcriptomic changes via RNAseq (Pezzini et al. 2017). 
-They then looked at functional enrichment of differentially expressed genes.
+## The question: What pathways are involved in SH-SY5Y Differentiation?
 
+In their paper [_Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells_](https://link.springer.com/article/10.1007%2Fs10571-016-0403-y), Pezzini et al. induced neuronal differentiation of the SH-SY5Y neuroblastoma cell line and measured transcriptomic changes using RNA sequencing (Pezzini et al. 2017). During the 9-day differentiation protocol, SH-SY5Y cells were initially pre-differentiated in a retinoic acid (RA) medium for 6 days, followed by a 3-day treatment with a neurobasal medium (NBM) enriched with neurotrophic factors. Control cells, which were not treated (NT), were maintained under basal conditions and served as a comparison group. The authors then performed functional enrichment analysis on the differentially expressed genes.
 
 ## The data : Differentially expressed genes
 
 The example dataset for today is the RNAseq differential expression results.  
 
-They can be accessed via this link: 
-http://degust.erc.monash.edu/degust/compare.html?code=5b2c7805ab8f8c5f2dc8c72e61b049b0#?plot=mds
+They can be accessed via this [Degust](http://degust.erc.monash.edu/degust/compare.html?code=5b2c7805ab8f8c5f2dc8c72e61b049b0#?plot=mds) link: 
 
 This has been reanalysed from the published raw data, via the degust tool. 
 
-> Note: Other tools and approaches will have different looking results - but generally you will end up with a table of genes with some measure of statistical confidence. 
-The methods for functional enrichment analysis should be similar.
+
+> **Note:** Other tools and approaches may produce different-looking results, but generally, you will end up with a table of genes containing some measure of statistical confidence. The methods for functional enrichment analysis should remain similar.
+

06-web-tools.Rmd

@@ -84,7 +84,10 @@ How can one perform Under Representation Analysis in gProfiler?
 <span style="color:orange;">- Run Query:</span> Same as above.
 
 #### **Challenge:** GSEA with gProfiler {- .challenge}
-Download the Hallmark gene sets ([h.all.v2024.1.Hs.symbols.gmt](https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2024.1.Hs/h.all.v2024.1.Hs.symbols.gmt)) from MSigDB and use it as Custom GMT.
+Download the Hallmark gene sets ([h.all.v2024.1.Hs.symbols.gmt](https://www.gsea-msigdb.org/)) from MSigDB and use it as Custom GMT.
+
+<!-- Full path to h.all.v2024.1.Hs.symbols.gmt -->
+<!-- [h.all.v2024.1.Hs.symbols.gmt](https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2024.1.Hs/h.all.v2024.1.Hs.symbols.gmt) -->
 
 #### **Question ** {- .rationale}
 
@@ -195,6 +198,9 @@ Clusters can be downloaded in `.tsv` format.
 #### **Question** {- .rationale}
 What was the overlap in enrichment terms between gProfiler and STRING at FDR ≤ 0.05?
 
+<!-- ### Steps to Perform GSEA in STRING: -->
+<!-- https://version-12-0.string-db.org/cgi/globalenrichment?networkId=bKhJ4fXp6sna -->
+
 <!-- ## FEA in [GenePattern](https://www.genepattern.org/#gsc.tab=0) -->
 ## FEA in GenePattern <a href="https://www.genepattern.org/#gsc.tab=0" target="_blank"><img src="images/GenePattern-logo.png" alt="GenePattern Logo" style="height:35px; vertical-align:middle;"></a>
 GenePattern, an online platform developed by the Broad Institute, offers a suite of tools for analyzing and visualizing genomic data, making bioinformatics accessible to researchers through a user-friendly, no-programming interface. Among its supported tools is Gene Set Enrichment Analysis (GSEA), which implements [MSigDB GSEA](https://www.gsea-msigdb.org/gsea/index.jsp) analysis for identifying enriched gene sets in genomic data. 
@@ -446,4 +452,5 @@ When running FEA in Reactome, how do you prefer the analysis methods?
 ####  {-}
 
 
+<!-- ## Evaluation Metrics for FEA Methods -->