GSEA Report for Dataset Normalized.FSHD2

Enrichment in phenotype: FSHD2 (5 samples)

• 505 / 1470 gene sets are upregulated in phenotype FSHD2
• 177 gene sets are significant at FDR < 25%
• 75 gene sets are significantly enriched at nominal pvalue < 1%
• 141 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: FSHD2M (5 samples)

• 965 / 1470 gene sets are upregulated in phenotype FSHD2M
• 472 gene sets are significantly enriched at FDR < 25%
• 229 gene sets are significantly enriched at nominal pvalue < 1%
• 347 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

Dataset details

• The dataset has 43120 features (genes)
• No probe set => gene symbol collapsing was requested, so all 43120 features were used

Gene set details

• Gene set size filters (min=15, max=500) resulted in filtering out 729 / 2199 gene sets
• The remaining 1470 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 FSHD2 versus FSHD2M comparison

• The dataset has 43120 features (genes)
• # of markers for phenotype FSHD2: 20924 (48.5% ) with correlation area 45.2%
• # of markers for phenotype FSHD2M: 22196 (51.5% ) with correlation area 54.8%
• 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: 43562 # of row UNIQUE ids in original dataset: 43120 # The duplicates were CD99 Metazoa_SRP 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 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 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 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA U3 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA 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 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA SNORA70 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA SNORA62 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 SNORA72 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA U3 Y_RNA Y_RNA Y_RNA SNORA70 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Metazoa_SRP Metazoa_SRP Metazoa_SRP 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 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA SNORA70 Y_RNA Y_RNA Y_RNA Y_RNA SNORA70 Y_RNA Y_RNA U8 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA SNORA72 Y_RNA SNORA70 Y_RNA Y_RNA 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 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 U3 U3 Y_RNA Y_RNA Y_RNA Y_RNA SNORA75 SNORA75 U3 SNORA75 Metazoa_SRP Metazoa_SRP 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 Y_RNA Y_RNA Y_RNA Metazoa_SRP U3 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA U8 Y_RNA U8 Y_RNA U8 Y_RNA U8 Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA Y_RNA SNORA70 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 Y_RNA Y_RNA Y_RNA Y_RNA SNORA70 Y_RNA SNORA73 ALG1L9P Metazoa_SRP ITFG2-AS1 LINC01238 GOLGA8M SNORD39 Metazoa_SRP TMSB15B U1 BMS1P4 U3 CYB561D2 SNORA62 SNORA74 Y_RNA POLR2J4 Metazoa_SRP Metazoa_SRP Metazoa_SRP U1 U1 Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP U1 U1 Metazoa_SRP Metazoa_SRP Metazoa_SRP Y_RNA Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP U2 Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Y_RNA Metazoa_SRP Metazoa_SRP U7 U1 Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Y_RNA Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Y_RNA Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Y_RNA Metazoa_SRP U1 Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP U1 Metazoa_SRP U1 Metazoa_SRP Metazoa_SRP U2 Metazoa_SRP U2 Metazoa_SRP Metazoa_SRP U4 Y_RNA Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP Metazoa_SRP MATR3 U6 U6 U6 U6 U6 U6 Metazoa_SRP U4 U6 Metazoa_SRP Y_RNA HSPA14 CCDC39 TBCE ATXN7 POLR2J3 SOD2 ZNF883 GGT1 AHRR ARMCX5-GPRASP2 C2orf27A