2.3. Output Contents (FastDTLgoea)

Output Contents

In this page, explain output contents of following 3 directories in 04_functional_analysis.

.
├── 00_user_data/  
├── 01_orthofinder/ 
├── 02_dtl_reconciliation/  
├── 03_aggregate_map_result/  
├── 04_functional_analysis/  -- GOEA(GO Enrichment Analysis) result
│   ├── go_annotation/   -- InterProScan GOterm annotation result 
│   ├── go_enrichment/   -- Gain/Loss gene GOEA result
│   └── result_summary/  -- GOEA summary result
└── log/

1. go_annotation/

go_annotation directory contains genomic CDSs InterProScan GOterm annotation files (*.tsv).

See InterProScan document for GOterm annotation file format details.

2. go_enrichment/

go_enrichment directory contains GOEA running work files.
All results are aggregated in result_summary directory.

3. result_summary/

result_summary contains 1 directory and 2 files.

• significant_go_plot/

  Significant GOterms plot figure files like below (See other example figures here).
  Default plot color is Yellow to Red gradient color. User can specify plot color by --plot_color option.

  

• significant_go_count.tsv

  Significant GOterms count file (See example data here).

  Columns	Content
  NODE_ID	NODE ID
  GAIN/LOSS	"gain" or "loss"
  GO_CATEGORY	"BP" or "MF" or "CC"
  OVER/UNDER	"over" or "under"
  SIGNIFICANT_GO_COUNT	Significant GOterm count
  SIGNIFICANT_GO_LIST	Significant GOterm list (e.g. GO:44237|GO:0071704)

• significant_go_list.tsv

  Significant GOterms list file (See example data here).

  Columns	Content
  NODE_ID	NODE ID
  GAIN/LOSS	"gain" or "loss"
  GO_CATEGORY	"BP" or "MF" or "CC"
  OVER/UNDER	"over" or "under"
  GO	GOterms ID
  GO_NAME	GOterms definition
  RATIO_IN_STUDY	Ratio in study (gain or loss)
  RATIO_IN_POP	Ratio in population
  PVALUE	P-value
  DEPTH	GOterm depth
  STUDY_COUNT	Study GOterms count
  BH_ADJUSTED_PVALUE	Benjamini-Hochberge adjusted P-value
  STUDY_ITEMS	Study GOterms list