PART II - Downstream analysis

4. MEME-CHIP for motif analysis of peaks

[ETC: analysis (10 mins) +  previous running (30 mins)]

• In your GALAXY session, to extract the sequence of the EWSR1-FLI1 peaks, run Genomic File Manipulation | BED | bedtools getfasta (source: Server indexed files, fasta_id: hg38) on the previous CrossMap output (in hg38)

• After, to identify motifs statistically conserved in these sequences, run Genomics Toolkits | Motif | MEME-ChIP on the previously retrieved sequences

Note: Results of this analysis can be downloaded directly from here

5. CHIP-ATLAS for enrichment peak analysis

[ETC: analysis (10 mins) +  previous runnings (20 mins)]

• Open the website of ChIP-ATLAS, click on the Enrichment Analysis tool

• Load the published set of peaks of EWSR1-FLI1 downloaded from GEO in the 4. Enter dataset A box

• Run two Enrichment analysis in parallel with the following 1. Experiment type boxes values:  ChIP: Histone and ChIP: TFs and others

6. ENRICHR for gene functional analysis

[ETC: 25 mins]

• Open again the publication on KDM6A and KDM6B [PMID:41085408]

• Access to the Supplementary Table S4 and copy the list of target genes of EWSR1-FLI1

• Open the Enrichr web site and analyze the target genes of KDM6A and KDM6B in parallel, using different libraries of the Transcription, Pathways and Ontologies blocks

• For the interesting results, change to the Table view mode to confirm the statistical values are significant

🚀 [TABLE OF CONTENTS OF THE COURSE] 🚀