GSEA Report for Dataset Placode

Enrichment in phenotype: KOD3.1 (2 samples)

• 4 / 4 gene sets are upregulated in phenotype KOD3.1
• 4 gene sets are significant at FDR < 25%
• 4 gene sets are significantly enriched at nominal pvalue < 1%
• 4 gene sets are significantly enriched at nominal pvalue < 5%
• Snapshot of enrichment results
• Detailed enrichment results in html format
• Detailed enrichment results in excel format (tab delimited text)
• Guide to interpret results

Enrichment in phenotype: WTD3.1 (2 samples)

• None of the gene sets are enriched in phenotype WTD3.1
• Guide to interpret results

Dataset details

• The dataset has 22468 features (genes)
• No probe set => gene symbol collapsing was requested, so all 22468 features were used

Gene set details

• Gene set size filters (min=15, max=2000) resulted in filtering out 0 / 4 gene sets
• The remaining 4 gene sets were used in the analysis
• List of gene sets used and their sizes (restricted to features in the specified dataset)

Gene markers for the KOD3.1 versus WTD3.1 comparison

• The dataset has 22468 features (genes)
• # of markers for phenotype KOD3.1: 11343 (50.5% ) with correlation area 53.3%
• # of markers for phenotype WTD3.1: 11125 (49.5% ) with correlation area 46.7%
• Detailed rank ordered gene list for all features in the dataset
• Heat map and gene list correlation profile for all features in the dataset

Global statistics and plots

• Plot of p-values vs. NES
• Global ES histogram

Other

• Parameters used for this analysis

Comments

• There were duplicate row identifiers in the specified dataset. One id was arbitarilly choosen. Details are below Generally, this is OK, but if you want to avoid this automagic, edit your dataset so that all row ids are unique # of row ids in original dataset: 22525 # of row UNIQUE ids in original dataset: 22468 # The duplicates were AC022400.1 AC026740.1 AC046143.2 AC078993.1 AC092811.1 AC093157.1 AC097658.1 AC132872.2 AF131215.5 AL136531.1 AL137127.1 ALG1L9P AP002495.1 BMS1P4 COG8 CYB561D2 DGCR5 EMG1 LINC01238 LYNX1 MAL2 MATR3 POLR2J4 RGS5 SNORA11 SNORA66 SNORA75 SNORA81 SNORD19 SNORD63 SOGA3 U3 U3 U3 U3 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA snoU13 snoU13 snoU13 snoU13 snoU13