Overview Fisher Exact test result¶

Data¶

Merged/unmerged m6A peaks， and unmerged m6A nonpeaks
RBP binding sites data (121 RBPs)
microRNA data (55 miRNA)

For microRNA data, some blocks (rows) have multi-binding-site. For example,

chr  start     end       name          strand   blockSize   blockStarts miRNA   name_gene
chr1    52260280    52260500    NRD1:miR-505-3p.1   -   2,6 0,214   hsa-miR-505-3p  NRD1
chr4    83346034    83346721    HNRNPDL:miR-140-3p.1 -  2,6 0,681   hsa-miR-140-3p  HNRNPDL
chr10   6261651 6262623  PFKFB3:miR-339-5p  +   5,3 0,969   hsa-miR-339-5p  PFKFB3

split the first row into separate rows

chr  start     end       name           strand  miRNA       name_gene   blockSize   interval
chr1    52260280    52260282    NRD1:miR-505-3p.1   -   hsa-miR-505-3p  NRD1    2           0
chr1    52260494    52260500    NRD1:miR-505-3p.1   -   hsa-miR-505-3p  NRD1    6           214

Perform Fisher's exact test for each RBP/miRNA over all chromosomes¶

Obtain 2 $\times$ 2 table for the test by bedtools

the number of intersection with m6A peaks
the total number of intersection with m6A peaks minus (1)
the number of intersection with m6A nonpeaks
the total number of intersection with m6A nonpeaks minus (3)

Pay attention to the potential m6A binding proteins (readers or anti-readers) include: YTHDF, HNRNP, FMRP, IGF2BP and G3BP. However, only HNRNP, FMR1 and IGF2BP are found in RBP dataset, including IGF2BP3, HNRNPUL1, HNRNPA1, HNRNPM, IGF2BP1, FMR1, HNRNPK, HNRNPU, IGF2BP2, HNRNPC.

Odds ratio and Fisher test p-value for RBPs¶

name    n_inter_peak    n_inter_nonpeak n_nointer_peak  n_nointer_nonpeak   fisher_p    odds_ratio
0   RBM15   5300    1565    859486  740576  0   2.91805
1   NCBP2   3198    1000    861588  741141  1.07934e-197    2.75093
2   DDX3X   5296    1726    859490  740415  4.69948e-307    2.64327
3   IGF2BP3 3947    1522    860839  740619  6.24384e-171    2.23113
4   FASTKD2 1647    717 863139  741424  1.04665e-55 1.97315
5   TRA2A   2553    1128    862233  741013  1.6042e-82  1.9451
6   DDX6    1416    631 863370  741510  1.68964e-45 1.92732
7   SLTM    1849    844 862937  741297  1.74622e-55 1.88195
8   FUS 103 47  864683  742094  0.000285908 1.88079
9   XRN2    2668    1239    862118  740902  7.36408e-76 1.85058
10  GTF2F1  3287    1587    861499  740554  1.67532e-83 1.78043
11  AUH 727 352 864059  741789  1.62622e-19 1.77308
12  RPS3    2794    1357    861992  740784  4.86427e-70 1.76944
13  FTO 9947    4991    854839  737150  1.57643e-222    1.71861
14  XRCC6   1259    638 863527  741503  1.32775e-28 1.6945
15  CSTF2T  7615    3889    857171  738252  5.34264e-161    1.68643
16  AGGF1   2042    1043    862744  741098  2.98371e-44 1.68176
17  LARP4   2150    1120    862636  741021  1.3017e-43  1.64901
18  GNL3    1761    919 863025  741222  8.65675e-36 1.64577
19  GEMIN5  7678    4023    857108  738118  9.47816e-149    1.64357
20  SF3B1   793 417 863993  741724  1.49165e-16 1.63256
21  DHX30   977 515 863809  741626  6.71227e-20 1.62875
22  NPM1    1186    626 863600  741515  1.01599e-23 1.62674
23  EIF4G2  7573    4052    857213  738089  3.40683e-136    1.60923
24  TAF15   3176    1724    861610  740417  5.46274e-55 1.5831
25  RPS11   1331    722 863455  741419  5.6842e-24  1.58294
26  PUS1    1279    697 863507  741444  9.74492e-23 1.57562
27  TROVE2  1463    810 863323  741331  2.35286e-24 1.55095
28  SBDS    904 503 863882  741638  2.41226e-15 1.5429
29  DDX55   2938    1652    861848  740489  1.94084e-44 1.52802
......

Odds ratio and Fisher test p-value for microRNAs¶

name    n_inter_peak    n_inter_nonpeak n_nointer_peak  n_nointer_nonpeak   p-value OR
0   hsa-miR-615-3p  6   1   4103    5579    0.0468574   8.15842
1   hsa-miR-423-3p  14  3   4095    5577    0.000993382 6.35556
2   hsa-miR-210-3p  12  3   4097    5577    0.00652049  5.44496
3   hsa-miR-127-3p  8   2   4101    5578    0.0223117   5.44062
4   hsa-miR-1249-3p 7   2   4102    5578    0.0422105   4.75939
5   hsa-miR-423-5p  58  37  4051    5543    0.000337447 2.14491
6   hsa-miR-212-5p  116 78  3993    5502    1.02772e-06 2.0492
7   hsa-miR-296-5p  63  43  4046    5537    0.000488117 2.00503
8   hsa-miR-328-3p  53  38  4056    5542    0.00268099  1.90573
9   hsa-miR-331-3p  52  40  4057    5540    0.0077257   1.7752
10  hsa-miR-491-5p  40  32  4069    5548    0.0305094   1.70435
11  hsa-miR-223-3p  101 82  4008    5498    0.000489454 1.6896
12  hsa-miR-140-3p  256 212 3853    5368    5.24253e-08 1.68235
13  hsa-miR-362-5p  38  33  4071    5547    0.0699765   1.56901
14  hsa-miR-143-3p  102 95  4007    5485    0.00859482  1.46972
15  hsa-miR-140-5p  94  88  4015    5492    0.0123344   1.46113
16  hsa-miR-132-3p  116 111 3993    5469    0.00798643  1.43134
17  hsa-miR-296-3p  11  11  4098    5569    0.520588    1.35896
18  hsa-miR-652-3p  4   4   4105    5576    0.729295    1.35834
19  hsa-miR-183-5p  232 240 3877    5340    0.00260642  1.33144
20  hsa-miR-532-3p  78  81  4031    5499    0.0897683   1.31365
21  hsa-miR-150-5p  64  67  4045    5513    0.154165    1.30189
22  hsa-miR-877-5p  22  23  4087    5557    0.450045    1.30056
23  hsa-miR-335-5p  51  55  4058    5525    0.237113    1.26249
24  hsa-miR-22-3p   131 143 3978    5437    0.0720579   1.25207
25  hsa-miR-142-3p  187 209 3922    5371    0.0486534   1.2253
26  hsa-miR-505-3p  105 117 4004    5463    0.149024    1.22445
27  hsa-miR-486-5p  28  32  4081    5548    0.514766    1.18954
28  hsa-miR-182-5p  223 262 3886    5318    0.108978    1.16479
29  hsa-miR-28-5p   38  45  4071    5535    0.577475    1.14812
30  hsa-miR-324-5p  27  32  4082    5548    0.600092    1.14677
31  hsa-miR-339-5p  36  43  4073    5537    0.569823    1.13814
32  hsa-miR-342-3p  48  58  4061    5522    0.554605    1.12532
33  hsa-miR-542-3p  53  72  4056    5508    1   0.99963
34  hsa-miR-874-3p  77  105 4032    5475    1   0.995784
35  hsa-miR-192-5p  30  42  4079    5538    1   0.969776
36  hsa-miR-744-5p  9   13  4100    5567    1   0.940019
37  hsa-miR-21-5p   52  76  4057    5504    0.719276    0.928246
38  hsa-miR-582-5p  82  120 4027    5460    0.615241    0.926496
39  hsa-miR-532-5p  34  53  4075    5527    0.586376    0.870091
40  hsa-miR-17-5p   231 370 3878    5210    0.045127    0.838765
41  hsa-miR-25-3p   134 216 3975    5364    0.122884    0.837149
42  hsa-miR-185-5p  63  107 4046    5473    0.159519    0.796446
43  hsa-miR-155-5p  68  116 4041    5464    0.132847    0.792634
44  hsa-miR-425-5p  38  66  4071    5514    0.232881    0.77984
45  hsa-miR-361-5p  34  60  4075    5520    0.248864    0.767607
46  hsa-miR-501-3p  23  42  4086    5538    0.260332    0.742221
47  hsa-miR-191-5p  9   18  4100    5562    0.436353    0.678293
48  hsa-miR-28-3p   15  30  4094    5550    0.230448    0.677821
49  hsa-miR-142-5p  100 206 4009    5374    0.000505664 0.65072
50  hsa-miR-221-3p  55  114 4054    5466    0.00941775  0.650495
51  hsa-miR-141-3p  116 239 3993    5341    0.000153408 0.649207
52  hsa-miR-340-5p  138 317 3971    5263    6.14614e-08 0.57697
53  hsa-miR-330-3p  241 589 3868    4991    1.28562e-16 0.527962
54  hsa-miR-186-5p  86  287 4023    5293    1.81417e-15 0.394247