Layers/Functional-annotations.md

 ---
 title: Functional annotations
 ---
+
 Functional annotation helps bringing biological meaning to genetic sequences. Functional annotation is usually obtained through protein sequence similarity. Indeed, across two organisms, if two sequences are very similar, one can infer that they can encode for the same biological function.
 There are several main parameters that will impact the process of functional annotation:
 - how distant is the species which was actually annotated with experimental data (the reference)
@@ -82,6 +83,35 @@ Perform as depicted on the picture above.
 15. Go to Export data
 16. Download the `Gene Family data` (`TRANSCRIPT WITH GF`)
 
+```
+#counter        transcript_id   gf_id
+6316    MtrunA17Chr2g0276741.1  4846_HOM04D004110
+6317    MtrunA17Chr2g0276751.1  4846_HOM04D000015
+6319    MtrunA17Chr2g0276781.1  
+6321    MtrunA17Chr2g0276801.1  4846_HOM04D008455
+```
+
+17. Download the `RNA Family data` (`TRANSCRIPT WITH RF`)
+
+```
+#counter        transcript_id   rf_id
+6316    MtrunA17Chr2g0276741.1  
+6317    MtrunA17Chr2g0276751.1  
+6319    MtrunA17Chr2g0276781.1
+```
+Few genes are annotated by this category.
+
+18. Download the `Gene Ontology data` (`TRANSCRIPT WITH GO`)
+
+```
+#counter        transcript_id   go      evidence_code   is_hidden       description
+1       MtrunA17Chr2g0327711.1  GO:0043229      ISS     1       intracellular organelle
+2       MtrunA17Chr2g0327711.1  GO:0070727      ISS     1       cellular macromolecule localization
+3       MtrunA17Chr2g0327711.1  GO:0009651      ISS     0       response to salt stress
+4       MtrunA17Chr2g0327711.1  GO:0008104      ISS     1       protein localization
+```
+`is_hidden` informs on whether the term is the most informative. If another more informative term annotates the gene, the term is hidden (1). This allows to reduce the number of effective annotations per gene and take advantage of the structure of the ontology instead.
+
 
 ## InterPro