Defintion of the fields in the ftp files? Where are the PCHi-C files?

For files under Index of /pub/databases/opentargets/genetics/latest/v2g/, what does each of the field mean? For instance, what’s interval score, what’s interval score q? Are these files of the same kind or different kinds?

Also, are the PCHi-C files available?

Thanks in advance!

Can anyone please help? Thanks!

Hi @Mousheng_Xu!

I have checked with the Genetics team, and they have told me the following regarding the fpred_scores, interval_score, and interval_score_q:

The fpred scores refer to VEP annotations.
interval_score refers to “interval”-type data that links regions to genes; this can include promoter-capture Hi-C data, DHS enhancer-promoter correlation, and FANTOM5 transcribed enhancer-promoter correlations.
interval_score likely refers to a raw score for the given data type, while interval_score_q is a quantile normalised score (i.e. 0 - 1).

As an example:

 alt_allele       | C                                              
 chr_id           | 5                                              
 d                | null                                           
 distance_score   | null                                           
 distance_score_q | null                                           
 feature          | unspecified                                    
 fpred_labels     | [upstream_gene_variant, intron_variant]        
 fpred_max_label  | intron_variant                                 
 fpred_max_score  | 0.1                                            
 fpred_scores     | [0.0, 0.1]                                     
 gene_id          | ENSG00000169194                                
 interval_score   | null                                           
 interval_score_q | null                                           
 position         | 132656919                                      
 qtl_beta         | null                                           
 qtl_pval         | null                                           
 qtl_score        | null                                           
 qtl_score_q      | null                                           
 qtl_se           | null                                           
 ref_allele       | A                                              
 source_id        | vep                                            
 type_id          | fpred