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==Enrichment in genomic regions== (A) Gene regions were taken from iGenome data which Rui downloaded: /media/1TB_store1/Rui_Scratch/iGenome/Mus_musculus/UCSC/mm9/Annotation/Genes [[File:refFlat.txt.gz]] File was parsed into five regions files using this script : [[File:parseRefFlat.txt]] mm9_ucsc_genes.3utr.bed - regions from coding start end to transcription end N = 28,108 sort -u | wc -l : 24,052 mm9_ucsc_genes.5utr.bed - regions from transcription start to coding start N = 28,108 sort -u | wc -l : 24,143 mm9_ucsc_genes.tss.bed - regions from -800 to +200 bp of transcription start N = 28,108 sort -u | wc -l : 23,652 mm9_ucsc_genes.exons.bed - coding regions N = 267,543 sort -u | wc -l : 208,522 mm9_ucsc_genes.introns.bed - non-coding regions (between every exons) N = 239,435 sort -u | wc -l : 186,730 **Performed sort -u on all files. (B) CpGIslands-regions.bed : downloaded from UCSC Table Browser for mm9 (C) mouseESp300binding_LICR_regions.bed : downloaded from UCSC Table Browser for mm9 (D) REST-binding_sites.bed (Repressor Element 1 Silencing Transcription Factor binding sites) : downloaded from UCSC Table Browser for mm9 ===Criteria for mapping to genomic regions=== *Count frequency of overlaps with a genomic region: For peaks: Total # bp overlapping with peaks For randomized regions: Total # bp overlapping with random regions ** Note Pastor et al required for larger regions that entire HERGs/MERGs fall within a larger genomic region. ===Criteria for randomized regions=== *Randomized regions conserve # peaks, chromosome distribution, and peak widths distribution. *Performed 1000 randomizations (Imputations). *Script: [[File:imputeRegionEnrichment.txt]] ===Results=== '''Control sample''' Total bp = 400,486bp {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Region_File''' | align="center" style="background:#f0f0f0;"|'''Test_counts''' | align="center" style="background:#f0f0f0;"|'''Imputed_ave''' | align="center" style="background:#f0f0f0;"|'''Imputed_std''' | align="center" style="background:#f0f0f0;"|'''Empirical_p (greater than)''' | align="center" style="background:#f0f0f0;"|'''Empirical_p (less than)''' |- | CpGIslands-regions.bed||5632||1754.636||973.5852||'''0'''||1 |- | mm9_ucsc_genes.3utr.bed||6782||12116.25||3978.4707||0.929||'''0.071''' |- | mm9_ucsc_genes.5utr.bed||22232||16190.186||4545.6284||'''0.087'''||0.913 |- | mm9_ucsc_genes.exons.bed||3856||9942.256||2401.9812||0.999||'''0.001''' |- | mm9_ucsc_genes.introns.bed||143652||149212.281||11603.9548||0.688||0.312 |- | mm9_ucsc_genes.tss.bed||4479||3729.626||1575.1404||0.296||0.704 |- | mouseESp300binding_LICR_regions.bed||6007||3879.494||1621.2735||0.112||0.888 |- | REST-binding_sites.bed||37||28.687||57.2239||0.238||0.762 |} *Control is '''enriched''' in CpG Islands and 5'UTR. *Control is '''depleted''' in 3'UTR and exons. '''Knock down''' Total bp = 220,304bp {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Region_File''' | align="center" style="background:#f0f0f0;"|'''Test_counts''' | align="center" style="background:#f0f0f0;"|'''Imputed_ave''' | align="center" style="background:#f0f0f0;"|'''Imputed_std''' | align="center" style="background:#f0f0f0;"|'''Empirical_p (greater than)''' | align="center" style="background:#f0f0f0;"|'''Empirical_p (less than)''' |- | CpGIslands-regions.bed||121||950.83||760.1284||0.876||0.124 |- | mm9_ucsc_genes.3utr.bed||4465||6457.113||2854.0275||0.742||0.258 |- | mm9_ucsc_genes.5utr.bed||5055||8971.008||3276.3609||0.891||0.109 |- | mm9_ucsc_genes.exons.bed||436||5460.863||1840.9045||1||'''0''' |- | mm9_ucsc_genes.introns.bed||86823||81022.857||8769.8664||0.248||0.752 |- | mm9_ucsc_genes.tss.bed||0||2064.625||1219.295||1||'''0''' |- | mouseESp300binding_LICR_regions.bed||1278||2084.766||1255.2735||0.707||0.293 |- | REST-binding_sites.bed||26||17.38||46.7585||0.169||0.831 |} *Knockdown is '''depleted''' at exons and tss.
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