Which are the promoters?

Question

[a511512345]

Hello everyone, I got some DNA regions with methylation differences, I am annotating the DNA region with wANNOVAR, and I get the following result, but I do not know if those regions are my desired promoter regions. Could you tell me? Very much looking forward to your reply, thank you

Chr Start   End Func.refGene    Gene.refGene
chr1    25257191    25258236    intronic    RSRP1
chr11   2397201 2397977 UTR3    CD81
chr6    31938372    31939112    ncRNA_intronic  C2-AS1
chr6    149805995   149806732   intronic    PCMT1
chr2    209224225   209225183   intergenic  LOC101927960;MAP2
chrY    6778641 6778641 intergenic  TTTY8;AMELY
chr14   76015669    76015669    intronic    IFT43
chr16   8995926 8995926 intergenic  USP7;C16orf72
chr18   77508326    77508326    intergenic  GALR1;LINC01029
chr11   13983009    13984067    intronic    SPON1
chr13   113776873   113777160   intronic    TMEM255B
chr10   43892790    43893015    ncRNA_intronic  LINC00840
chr2    177003406   177004015   intergenic  LINC01117;HNRNPA3
chr7    4848683 4848939 intronic    RADIL
chr11   75139390    75139736    intergenic  OR2AT4;SLCO2B1
chr5    158523507   158524404   intergenic  LINC02227;EBF1
chr5    179740743   179741120   intronic    MAML1
chr18   21572622    21572748    intronic    ESCO1
chr13   113426250   113426343   intronic    ADPRHL1
chr11   69919990    69920437    intergenic  FGF3;LOC101928443
chr8    67975874    67975895    intronic    PREX2
chr10   130832268   130832393   intergenic  GLRX3;MIR378C
chr8    129061191   129061665   intergenic  LINC00976;LINC00977
chr4    122721721   122721982   intergenic  IL21-AS1;CETN4P
chr10   43891459    43891547    ncRNA_intronic  LINC00840
chr2    11606945    11607042    intronic    GREB1
chr16   88988174    88988235    intergenic  CBFA2T3;ACSF3
chr12   116996871   116997535   intronic    FBXW8
chr10   102821552   102822249   intergenic  WBP1L;CYP17A1
chr20   19915716    19916087    intronic    RIN2
chr19   15343170    15343395    intergenic  BRD4;AKAP8
chr10   729479  729956  intergenic  DIP2C;LARP4B
chr22   22901830    22902237    intergenic  IGLL5;RSPH14
chr17   46698273    46699155    intronic    NSF
chr6    32805398    32805692    intergenic  HLA-DQB2;HLA-DOB
chr2    176978289   176979788   intergenic  LINC01117;HNRNPA3
chr20   61200716    61201650    intergenic  LINC01718;CDH4
chr13   76444798    76445065    intergenic  LMO7DN;KCTD12
chr1    3147329 3147966 intronic    PRDM16
chr4    123747447   123747672   ncRNA_intronic  LINC01091
chr16   30485485    30485810    intronic    ITGAL
chr16   86016317    86016387    intergenic  IRF8;LINC01082
chr10   134143489   134143535   intergenic  NONE;NONE
chr7    2548137 2548262 intronic    BRAT1
chr7    25702709    25702848    intergenic  NPVF;MIR148A
chr13   25290701    25290781    intergenic  MTMR6;NUP58
chr21   36577539    36577638    upstream    CLDN14

Answer 1

[Devon Ryan]

The ones with upstream in column 4 are promoter regions. Note that annovar uses a 1kb region for upstream by default.

Keep in mind that annovar is probably not an ideal tool to use for this. For example, if you have a DMR overlapping a promoter that also partially overlaps an exon then it'll be labeled exonic. What would be more useful is to take a BED file of promoters (either download from biomart or make one) and simply bedtools intersect that with your DMRs. Then you know exactly what intersects with which promoter (and by how much).

[a511512345]

thank you very much. I will try it