[1]:
import tfcomb.annotation
import pandas as pd
pd.set_option("display.max_columns", 50)
Annotate binding sites to genes
We will start by reading in known co-occurring rules:
[2]:
C = tfcomb.CombObj().from_pickle("../data/GM12878_selected.pkl")
[3]:
C.rules.head(20)
[3]:
| TF1 | TF2 | TF1_TF2_count | TF1_count | TF2_count | cosine | zscore | |
|---|---|---|---|---|---|---|---|
| CTCF-RAD21 | CTCF | RAD21 | 1751 | 2432 | 2241 | 0.750038 | 18.643056 |
| RAD21-SMC3 | RAD21 | SMC3 | 1376 | 2241 | 1638 | 0.718192 | 20.314026 |
| CTCF-SMC3 | CTCF | SMC3 | 1361 | 2432 | 1638 | 0.681898 | 20.245177 |
| IKZF1-IKZF2 | IKZF1 | IKZF2 | 1726 | 2922 | 2324 | 0.662343 | 11.215960 |
| SMC3-ZNF143 | SMC3 | ZNF143 | 1060 | 1638 | 1652 | 0.644383 | 21.838431 |
| FOS-NFYA | FOS | NFYA | 19 | 45 | 21 | 0.618070 | 58.099184 |
| BATF-JUNB | BATF | JUNB | 1135 | 1854 | 1866 | 0.610218 | 15.351205 |
| RAD21-ZNF143 | RAD21 | ZNF143 | 1136 | 2241 | 1652 | 0.590408 | 15.168180 |
| CTCF-ZNF143 | CTCF | ZNF143 | 1170 | 2432 | 1652 | 0.583713 | 15.459923 |
| CREB1-CREM | CREB1 | CREM | 717 | 1114 | 1392 | 0.575780 | 26.936982 |
| ATF2-NFIC | ATF2 | NFIC | 957 | 1484 | 1911 | 0.568283 | 14.789330 |
| USF1-USF2 | USF1 | USF2 | 136 | 259 | 249 | 0.535537 | 36.979279 |
| SMC3-TRIM22 | SMC3 | TRIM22 | 906 | 1638 | 1786 | 0.529701 | 13.521569 |
| MEF2A-MEF2C | MEF2A | MEF2C | 425 | 1129 | 572 | 0.528864 | 26.006588 |
| TCF12-TCF3 | TCF12 | TCF3 | 407 | 884 | 688 | 0.521884 | 28.784395 |
| BCL11A-IRF4 | BCL11A | IRF4 | 522 | 1009 | 994 | 0.521233 | 22.614173 |
| ATF2-CREM | ATF2 | CREM | 742 | 1484 | 1392 | 0.516259 | 15.723393 |
| FOXM1-NFIC | FOXM1 | NFIC | 750 | 1115 | 1911 | 0.513799 | 20.462765 |
| HCFC1-SIX5 | HCFC1 | SIX5 | 111 | 287 | 172 | 0.499595 | 35.818992 |
| ATF2-FOXM1 | ATF2 | FOXM1 | 638 | 1484 | 1115 | 0.495982 | 16.925349 |
We then use get_pair_locations to get the locations of the co-occurring sites:
[4]:
locations = C.get_pair_locations(("JUNB", "BATF"))
INFO: Setting up binding sites for counting
[5]:
type(locations)
[5]:
tfcomb.utils.TFBSPairList
[6]:
len(locations)
[6]:
1135
We can show these locations as a table using .as_table:
[7]:
location_table = locations.as_table()
location_table
[7]:
| site1_chrom | site1_start | site1_end | site1_name | site1_score | site1_strand | site2_chrom | site2_start | site2_end | site2_name | site2_score | site2_strand | site_distance | site_orientation | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr4 | 699544 | 699545 | BATF | 1000 | . | chr4 | 699546 | 699547 | JUNB | 791 | . | 1 | NA |
| 1 | chr4 | 799162 | 799163 | BATF | 1000 | . | chr4 | 799177 | 799178 | JUNB | 1000 | . | 14 | NA |
| 2 | chr4 | 924255 | 924256 | JUNB | 1000 | . | chr4 | 924307 | 924308 | BATF | 1000 | . | 51 | NA |
| 3 | chr4 | 1218967 | 1218968 | BATF | 1000 | . | chr4 | 1218986 | 1218987 | JUNB | 1000 | . | 18 | NA |
| 4 | chr4 | 1710533 | 1710534 | BATF | 1000 | . | chr4 | 1710546 | 1710547 | JUNB | 718 | . | 12 | NA |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 1130 | chr4 | 185788438 | 185788439 | BATF | 1000 | . | chr4 | 185788469 | 185788470 | JUNB | 1000 | . | 30 | NA |
| 1131 | chr4 | 186134462 | 186134463 | BATF | 1000 | . | chr4 | 186134479 | 186134480 | JUNB | 1000 | . | 16 | NA |
| 1132 | chr4 | 186839676 | 186839677 | JUNB | 1000 | . | chr4 | 186839701 | 186839702 | BATF | 1000 | . | 24 | NA |
| 1133 | chr4 | 189503100 | 189503101 | JUNB | 1000 | . | chr4 | 189503109 | 189503110 | BATF | 744 | . | 8 | NA |
| 1134 | chr4 | 189631410 | 189631411 | BATF | 1000 | . | chr4 | 189631459 | 189631460 | JUNB | 1000 | . | 48 | NA |
1135 rows × 14 columns
Annotate regions
We can now use annotate_regions to annotate these locations to genes:
[8]:
annotated = tfcomb.annotation.annotate_regions(location_table, gtf="../data/chr4_genes.gtf")
[W::hts_idx_load2] The index file is older than the data file: ../data/chr4_genes.gtf.gz.tbi
[9]:
annotated
[9]:
| site1_chrom | site1_start | site1_end | site1_name | site1_score | site1_strand | site2_chrom | site2_start | site2_end | site2_name | site2_score | site2_strand | site_distance | site_orientation | feature | feat_strand | feat_start | feat_end | query_name | distance | feat_anchor | feat_ovl_peak | peak_ovl_feat | relative_location | gene_id | gene_version | gene_name | gene_source | gene_biotype | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr4 | 699544 | 699545 | BATF | 1000 | . | chr4 | 699546 | 699547 | JUNB | 791 | . | 1 | NA | gene | + | 705747.0 | 770640.0 | query_1 | 6203.0 | start | 0.0 | 0.0 | Upstream | ENSG00000185619 | 18 | PCGF3 | ensembl_havana | protein_coding |
| 1 | chr4 | 799162 | 799163 | BATF | 1000 | . | chr4 | 799177 | 799178 | JUNB | 1000 | . | 14 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 2 | chr4 | 924255 | 924256 | JUNB | 1000 | . | chr4 | 924307 | 924308 | BATF | 1000 | . | 51 | NA | gene | + | 932386.0 | 958656.0 | query_1 | 8131.0 | start | 0.0 | 0.0 | Upstream | ENSG00000127419 | 17 | TMEM175 | ensembl_havana | protein_coding |
| 3 | chr4 | 1218967 | 1218968 | BATF | 1000 | . | chr4 | 1218986 | 1218987 | JUNB | 1000 | . | 18 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 4 | chr4 | 1710533 | 1710534 | BATF | 1000 | . | chr4 | 1710546 | 1710547 | JUNB | 718 | . | 12 | NA | gene | + | 1712857.0 | 1745171.0 | query_1 | 2324.0 | start | 0.0 | 0.0 | Upstream | ENSG00000013810 | 21 | TACC3 | ensembl_havana | protein_coding |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 1130 | chr4 | 185788438 | 185788439 | BATF | 1000 | . | chr4 | 185788469 | 185788470 | JUNB | 1000 | . | 30 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 1131 | chr4 | 186134462 | 186134463 | BATF | 1000 | . | chr4 | 186134479 | 186134480 | JUNB | 1000 | . | 16 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 1132 | chr4 | 186839676 | 186839677 | JUNB | 1000 | . | chr4 | 186839701 | 186839702 | BATF | 1000 | . | 24 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 1133 | chr4 | 189503100 | 189503101 | JUNB | 1000 | . | chr4 | 189503109 | 189503110 | BATF | 744 | . | 8 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 1134 | chr4 | 189631410 | 189631411 | BATF | 1000 | . | chr4 | 189631459 | 189631460 | JUNB | 1000 | . | 48 | NA | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
1135 rows × 29 columns
By subsetting all sites, we can highlight the pairs annotated to promoters of any genes:
[10]:
annotated[~annotated["gene_id"].isna()]
[10]:
| site1_chrom | site1_start | site1_end | site1_name | site1_score | site1_strand | site2_chrom | site2_start | site2_end | site2_name | site2_score | site2_strand | site_distance | site_orientation | feature | feat_strand | feat_start | feat_end | query_name | distance | feat_anchor | feat_ovl_peak | peak_ovl_feat | relative_location | gene_id | gene_version | gene_name | gene_source | gene_biotype | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr4 | 699544 | 699545 | BATF | 1000 | . | chr4 | 699546 | 699547 | JUNB | 791 | . | 1 | NA | gene | + | 705747.0 | 770640.0 | query_1 | 6203.0 | start | 0.0 | 0.0 | Upstream | ENSG00000185619 | 18 | PCGF3 | ensembl_havana | protein_coding |
| 2 | chr4 | 924255 | 924256 | JUNB | 1000 | . | chr4 | 924307 | 924308 | BATF | 1000 | . | 51 | NA | gene | + | 932386.0 | 958656.0 | query_1 | 8131.0 | start | 0.0 | 0.0 | Upstream | ENSG00000127419 | 17 | TMEM175 | ensembl_havana | protein_coding |
| 4 | chr4 | 1710533 | 1710534 | BATF | 1000 | . | chr4 | 1710546 | 1710547 | JUNB | 718 | . | 12 | NA | gene | + | 1712857.0 | 1745171.0 | query_1 | 2324.0 | start | 0.0 | 0.0 | Upstream | ENSG00000013810 | 21 | TACC3 | ensembl_havana | protein_coding |
| 13 | chr4 | 2761381 | 2761382 | JUNB | 855 | . | chr4 | 2761397 | 2761398 | BATF | 1000 | . | 15 | NA | gene | - | 2741647.0 | 2756342.0 | query_1 | 5039.0 | start | 0.0 | 0.0 | Upstream | ENSG00000168884 | 15 | TNIP2 | ensembl_havana | protein_coding |
| 15 | chr4 | 2787533 | 2787534 | BATF | 1000 | . | chr4 | 2787566 | 2787567 | JUNB | 954 | . | 32 | NA | gene | + | 2793070.0 | 2841098.0 | query_1 | 5537.0 | start | 0.0 | 0.0 | Upstream | ENSG00000087266 | 17 | SH3BP2 | ensembl_havana | protein_coding |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 1106 | chr4 | 184734256 | 184734257 | BATF | 1000 | . | chr4 | 184734285 | 184734286 | JUNB | 580 | . | 28 | NA | gene | - | 184694084.0 | 184734130.0 | query_1 | 126.0 | start | 0.0 | 0.0 | Upstream | ENSG00000151725 | 12 | CENPU | ensembl_havana | protein_coding |
| 1117 | chr4 | 185205229 | 185205230 | BATF | 607 | . | chr4 | 185205254 | 185205255 | JUNB | 878 | . | 24 | NA | gene | + | 185204236.0 | 185370185.0 | query_1 | 993.0 | start | 1.0 | 0.000006 | PeakInsideFeature | ENSG00000109762 | 16 | SNX25 | ensembl_havana | protein_coding |
| 1124 | chr4 | 185399224 | 185399225 | JUNB | 1000 | . | chr4 | 185399267 | 185399268 | BATF | 1000 | . | 42 | NA | gene | - | 185363871.0 | 185395924.0 | query_1 | 3300.0 | start | 0.0 | 0.0 | Upstream | ENSG00000109771 | 16 | LRP2BP | ensembl_havana | protein_coding |
| 1125 | chr4 | 185405783 | 185405784 | JUNB | 1000 | . | chr4 | 185405801 | 185405802 | BATF | 1000 | . | 17 | NA | gene | - | 185363871.0 | 185395924.0 | query_1 | 9859.0 | start | 0.0 | 0.0 | Upstream | ENSG00000109771 | 16 | LRP2BP | ensembl_havana | protein_coding |
| 1127 | chr4 | 185479574 | 185479575 | BATF | 1000 | . | chr4 | 185479580 | 185479581 | JUNB | 1000 | . | 5 | NA | gene | - | 185445181.0 | 185471752.0 | query_1 | 7822.0 | start | 0.0 | 0.0 | Upstream | ENSG00000168491 | 10 | CCDC110 | ensembl_havana | protein_coding |
94 rows × 29 columns