Web page legend:

Overall family annotations:

Family id: prefix of UTRP for UTR with paralog set; GW for genome-wide set; GWP for genome-wide with paralog set

Rank: family ranked position by independent compensatory double substitution evidence

Mean len: mean length of family members

P dbl(used): "p-value" for family based on combined compensatory double substitution evidence of family members (based on species used for inference)

P dbl(indep): p-value for family based on combined compensatory double substitution evidence of family members (based on independent species not used for inference) (Note: 2 indicates fully conserved; 3 indicates chr M homology)

P region: p-value based on overal enrichment of family members for a particular genomic region

BP: Gene ontology biological process enrichment for family, relative to set of all EvoFold predictions.

MF: Gene ontology metabolic function enrichment for family, relative to set of all EvoFold predictions.

CC: Gene ontology cellular content enrichment for family, relative to set of all EvoFold predictions.

KEGG: KEGG pathway enrichment of family (not currently computed)

P imm: enrichment for family members to be in macrophage-related immune genes

P strand: enrichment for family member structures to be located on coding strand of enclosing gene where applicable  

 

Family member annotations:

id: EvoFold prediction identifier

chr: chromosome

str: strand on which EvoFold predicted the structure

gstr: coding strand for protein-coding genes, otherwise NA (not available)

qual: "p-value" for compensatory double substitution evidence, calculated on species used for inference

quali: p-value for compensatory double substitution evidence, calculated on an independent set of species not used for inference

css: number of compatible single substitutions (dependent set)

shape: RNA structure shape. A schematic diagram: [] for hairpin, [][][] for cloverleaf etc.

loc: genomic location-- UTR5 (5'UTR), UTR3 (3'UTR), intron, or intergenic

fnRNA: known annotated functional RNAs that overlap, based on RFAM, mirBase etc

sym: gene symbol (HGNC when assigned)

desc: gene description

imm: macrophage-related gene, based on Innate Immune Database

linc: overlaps long intervening noncoding RNA (linc-RNA)

repeats: in a repeat region

bp: GO biological process annotations

mf: GO metabolic function annotations

cc: GO cellular content annotations

 

Notes:

Turn on the EvoFold_v.7b.3  and EvoFold_paralogs tracks from the “Genes and Gene Prediction Tracks” section of the genome browser to examine structures.

EvoFold ids ending in “_0” are the result of paralog search from the original EvoFold predictions.

All coordinates relative to UCSC hg18 assembly.