Hackseq Project #5
Evaluating epigenetic modifications in ChIP-seq and methylation data across cell types and states
Tools of interest
Motif finding in DMR
Top matches for known motifs in the down-methylated regions | |||||||
pattern | sequence name | start | stop | score | p-value | q-value | matched sequence |
MA0528.1 | chr7:108066562-108067006 | 206 | 226 | 29.4898 | 4.92E-13 | 6.52E-08 | GGAGGAGGAGGAGGAGGAGGG |
MA0528.1 | chr4:56875392-56877360 | 233 | 253 | 29.449 | 5.95E-13 | 6.52E-08 | ggaggaggaggaggaggagga |
MA0528.1 | chr4:56875392-56877360 | 236 | 256 | 29.449 | 5.95E-13 | 6.52E-08 | ggaggaggaggaggaggagga |
MA0528.1 | chr4:56875392-56877360 | 239 | 259 | 29.449 | 5.95E-13 | 6.52E-08 | ggaggaggaggaggaggagga |
MA0528.1 | chr4:56875392-56877360 | 242 | 262 | 29.449 | 5.95E-13 | 6.52E-08 | ggaggaggaggaggaggagga |
MA0528.1 | chr4:56875392-56877360 | 245 | 265 | 29.449 | 5.95E-13 | 6.52E-08 | ggaggaggaggaggaggagga |
Top motif found by occurence (down-methylated regions) |
5861 MA0528.1 |
2816 MA0073.1 |
2626 MA0149.1 |
2062 MA0472.1 |
1620 MA0516.1 |
1596 MA0050.2 |
1566 MA0079.3 |
1505 MA0474.1 |
1378 MA0098.2 |
Top motif found by occurence (up-methylated regions) |
5418 MA0528.1 |
3599 MA0554.1 |
2167 MA0073.1 |
2114 MA0149.1 |
1932 MA0543.1 |
1441 MA0079.3 |
1431 MA0516.1 |
1324 MA0753.1 |
1278 MA0537.1 |
De novo motif discovery in DMR
Arid3b - MA0601.1 | Alignment | |
Database | JASPAR CORE 2016 | |
p-value | 9.20e-05 | |
E-value | 9.95e-02 | |
q-value | 5.88e-02 | |
Overlap | 10 | |
Offset | 1 | |
Orientation | Reverse Complemen |
SPIC - MA0687.1 | Alignment | |
Database | JASPAR CORE 2016 | |
p-value | 8.59e-07 | |
E-value | 9.30e-04 | |
q-value | 1.86e-03 | |
Overlap | 13 | |
Offset | 1 | |
Orientation | Normal |
Top scoring motif in
1) Full DMR regions (Arid3b)
2) In hypermethylated regions discriminating against hypomethylated regions.
Peak enrichment analysis
See RMarkdown (meth_to_tf.rmd) document in the repository!
Gene annotations
CDK6 known to be involved in HSC quiescence
Checked in RNA-seq: 1.45-fold higher expression in young mice
Mir-101c also implicated in leukemias
Gene annotations