Think about comparison with ancestral reconstruction MPRAs

[petercombs]

Klein et al have published STARR-seq data with some ancestral reconstruction of enhancers.

1. Do any of their enhancers overlap with the ones in the Kirchner data?

2. Do we see selection in the branches that most correspond to the enhancers that are specifically expressing in certain taxa? Presumably we will have lower-than-chance overlap with the enhancers that express in non-humans, since the Kirchner enhancers weren't randomly chosen, but that's okay.

[petercombs]

Looks like this won't actually work, since we have exactly zero overlaps (even after converting data to the same reference coordinates):

$ bedtools closest -a kirchner.bed -b klein_all_hg38.bed -d  | column -t
1   109274651  109275251  SORT1-flip     1   109895959  109896145  620709
1   109274652  109275251  SORT1          1   109895959  109896145  620709
1   109274652  109275251  SORT1.2        1   109895959  109896145  620709
1   155301395  155301864  PKLR-24h       1   151002805  151002988  4298408
1   155301395  155301864  PKLR-48h       1   151002805  151002988  4298408
1   209815790  209816390  IRF6           1   211616739  211616925  1800350
10  43086479   43087078   RET            10  71342543   71342725   28255466
10  46046244   46046834   MSMB           10  71342543   71342725   25295710
10  112998240  112998839  TCF7L2         10  100341257  100341443  12656798
11  5227022    5227208    HBB            11  1988198    1988384    3238639
11  5249805    5250078    HBG1           11  1988198    1988384    3261422
19  11089231   11089548   LDLR           19  7398818    7399004    3690228
19  11089231   11089548   LDLR.2         19  7398818    7399004    3690228
2   60494940   60495539   BCL11A         2   47074762   47074947   13419994
2   161238408  161238998  UC88           2   134457866  134458047  26780362
20  44355520   44355804   HNF4A          20  48373754   48373940   4017951
22  19723266   19723650   GP1BA          22  19892087   19892273   168438
5   1294989    1295247    TERT-GAa       5   1563189    1563375    267943
5   1294989    1295247    TERT-GBM       5   1563189    1563375    267943
5   1294989    1295247    TERT-GSc       5   1563189    1563375    267943
5   1294989    1295247    TERT-HEK       5   1563189    1563375    267943
6   396143     396593     IRF4           6   7137078    7137253    6740486
6   37807499   37808077   ZFAND3         6   36127549   36127734   1679766
7   156791119  156791604  ZRSh-13        7   99372645   99372831   57418289
7   156791119  156791604  ZRSh-13h2      7   99372645   99372831   57418289
8   127400829  127401428  MYCrs6983267   8   128176976  128177162  775549
8   127519270  127519732  MYCrs11986220  8   128176976  128177162  657245
9   97853255   97853854   FOXE1          9   114118163  114118348  16264310
X   139530463  139530765  F9             .   -1         -1         -1

In some cases we get as close as 170kb, but that's not really the same thing, now is it.