Top FDR-corrected gene sets from GSEA in discovery and replication cohort
| Gene set name . | FDR value . | Significant genes/all genes . | ENCODE-enriched peaks . |
|---|---|---|---|
| Discovery cohort | |||
| GO: REGULATION OF ORGANELLE ORGANIZATION AND BIOGENESIS | 0.0030 | 34/40 | 210 |
| KEGG: T CELL RECEPTOR SIGNALING PATHWAY | 0.0046 | 80/108 | 699 |
| GO: MICROTUBULE BASED PROCESS | 0.0047 | 59/82 | 382 |
| GO: OXIDOREDUCTASE ACTIVITY GO 0016616 | 0.0048 | 40/58 | 261 |
| GO: NEGATIVE REGULATION OF DEVELOPMENTAL PROCESS | 0.0049 | 146/197 | 649 |
| Replication cohort | |||
| GO: CARBOHYDRATE CATABOLIC PROCESS | 0.0037 | 18/24 | 13 |
| KEGG: DRUG METABOLISM CYTOCHROME P450 | 0.0038 | 61/72 | 148 |
| GO: METAL ION TRANSPORT | 0.0040 | 91/117 | 621 |
| GO: CELLULAR CARBOHYDRATE CATABOLIC PROCESS | 0.0041 | 17/23 | 13 |
| KEGG: STARCH AND SUCROSE METABOLISM | 0.0041 | 43/52 | 0 |
| Gene set name . | FDR value . | Significant genes/all genes . | ENCODE-enriched peaks . |
|---|---|---|---|
| Discovery cohort | |||
| GO: REGULATION OF ORGANELLE ORGANIZATION AND BIOGENESIS | 0.0030 | 34/40 | 210 |
| KEGG: T CELL RECEPTOR SIGNALING PATHWAY | 0.0046 | 80/108 | 699 |
| GO: MICROTUBULE BASED PROCESS | 0.0047 | 59/82 | 382 |
| GO: OXIDOREDUCTASE ACTIVITY GO 0016616 | 0.0048 | 40/58 | 261 |
| GO: NEGATIVE REGULATION OF DEVELOPMENTAL PROCESS | 0.0049 | 146/197 | 649 |
| Replication cohort | |||
| GO: CARBOHYDRATE CATABOLIC PROCESS | 0.0037 | 18/24 | 13 |
| KEGG: DRUG METABOLISM CYTOCHROME P450 | 0.0038 | 61/72 | 148 |
| GO: METAL ION TRANSPORT | 0.0040 | 91/117 | 621 |
| GO: CELLULAR CARBOHYDRATE CATABOLIC PROCESS | 0.0041 | 17/23 | 13 |
| KEGG: STARCH AND SUCROSE METABOLISM | 0.0041 | 43/52 | 0 |
The GSEA package lists regulatory elements from ENCODE (Encyclopedia of DNA Elements) projects. The “ENCODE-enriched peaks” column contains the number of statistically significant peaks (P < .05) identified in each gene set. The enrichment peaks were obtained from DNase-seq, FAIRE-Seq (formaldehyde-assisted isolation of regulatory elements), TFBS (transcription factor binding sites) chromatin immunoprecipitation sequencing (ChIP)-seq, and histone ChIP-seq within the ENCODE project.