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BixBench item

bix-43-q4

Question

After performing differential gene expression analysis comparing CBD/cisplatin treatment vs DMSO control (using padj < 0.05 and |log2FC| ≥ 0.5), followed by enrichment analysis using gseapy with Reactome_2022 gene sets, what is the overlap ratio (DEGs found in pathway / total pathway genes) for the 'TP53 Regulates Transcription Of Cell Cycle Genes' pathway in the enrichment results? Express your answer as a fraction (e.g., X/Y).

Ideal answer
8/49
Category
RNA-seq,Differential Expression Analysis,Transcriptomics

Galaxy-API code with skills

3/3 pass

Galaxy-API code without skills

3/3 pass

Open-ended code with skills

3/3 pass

replicate 1

pass
Answer8/49
Workflow
local codePyDESeq2GSEApyEnrichrReactome
No Galaxy historyHugging Face trace

replicate 2

pass
Answer8/49
Workflow
local codeDESeq2GSEApyReactome
No Galaxy historyHugging Face trace

replicate 3

pass
Answer8/49
Workflow
local codePyDESeq2GSEApyEnrichrReactome
No Galaxy historyHugging Face trace

Open-ended code without skills

3/3 pass

replicate 1

pass
Answer8/49
Workflow
local codeGSEApyEnrichrReactome
No Galaxy historyHugging Face trace

replicate 2

pass
Answer8/49
Workflow
local codePyDESeq2GSEApyEnrichrReactome
No Galaxy historyHugging Face trace

replicate 3

pass
Answer8/49
Workflow
local codeDESeq2GSEApyReactome
No Galaxy historyHugging Face trace