High-confidence active/inactive segments

Following are segments whose state assignments agree across all 5 different segmentations.

1. one-track segmentation of 51.2kb wavelet-smoothed Affy RNA
2. one-track segmentation of 64kb wavelet-smoothed Sanger H3ac
3. one-track segmentation of 64kb wavelet-smoothed UCSD H3K27me3
4. one-track segmentation of TR50
5. four-track segmentation of all of the above

Specifically, coordinates of the "Active" segments below fell in state 1 for the four-track, H3ac, and Affy segmentations, and in state 0 for H3K27me3 and TR50. Coordinates of the "Inactive" segments fell in state 0 for the four-track, H3ac, and Affy segmenations, and in state 1 for H3K27me3 and TR50.

• Active: UCSC, BED
• Inactive: UCSC, BED
• Both: UCSC, WIG

Active/Inactive segment statistics

• Number of segments
• Inactive: 43
• Active: 51
• Total size (bp)
• Inactive: 4241811
• Active: 6086065
• Avg. segment length
• Inactive: 98647
• Active: 119335
• Median segment length
• Inactive: 73999
• Active: 72775
• Minimum segment length
• Inactive: 2599
• Active: 1174
• Maximum segment length
• Inactive: 306283
• Active: 495865

Gene overlap

Bed files below contain one line for each gene whose Tx start sits inside the given state. Columns are chr, start, stop, gene ID, fraction of gene sitting inside the segment, strand, and segment ID

• Overlap with active state
• GO term analysis -- biological process
• GO term analysis -- molecular function
• GO term analysis -- cellular components
• Overlap with inactive state
• GO term analysis -- biological process
• GO term analysis -- molecular function
• GO term analysis -- cellular components

Enrichment/depletion of various elements

Enrichment p-values are computed by permuting state labels on the fixed segmentation 10000 times, with adjusted p-values using method "BH".

Element                                        inactive         active   inact enr   inact enr p   inact adj p     act enr    act enr p    act adj p
-------------------------                  ------------   ------------   ---------   -----------   -----------   ---------   ----------   ----------
Num_Gencode_TxStarts                                196           1339      -0.512         0.001      0.002462       1.326            0            0
Num_mRNA_TxStarts                                   346           2703      -0.494        0.0237       0.03992       1.753            0            0
Num_Spliced.EST_TxStarts                           8168          96898      -0.583        0.1498        0.1917       2.449            0            0
EST_Ovr                                         2619036        4836685      -0.053        0.2387        0.2829       0.219            0            0
CpG.UCSC_Isl_Ovr                                   6709         172629      -0.880             0             0       1.153            0            0
RptMskr_Ovr                                     1887499        2751102      -0.013        0.3224        0.3439       0.003        0.465         0.48
RptMskr_DNA_Ovr                                  116887         121057       0.001         0.494         0.494      -0.277            0            0
RptMskr_LINE.L1_Ovr                              700111         494945       0.173        0.0196       0.03689      -0.422            0            0
RptMskr_LINE.L2_Ovr                              172048         176078       0.207        0.0014      0.002987      -0.139       0.0277      0.04233
RptMskr_LTR_Ovr                                  340543         244932       0.137        0.0291       0.04233      -0.430            0            0
RptMskr_SINE.ALU_Ovr                             304553        1436181      -0.440        0.0002     0.0005818       0.840            0            0
SimpRep_Ovr                                       91268         167620      -0.142         0.215        0.2646       0.098       0.3131       0.3439
MSA_strict_Ovr                                    76840         205982      -0.242        0.0341       0.04744       0.416       0.0012     0.002743
MSA_moderate_Ovr                                 170597         402256      -0.184        0.0473       0.06307       0.341       0.0007     0.001867
MSA_loose_Ovr                                    430412         859687      -0.139         0.029       0.04233       0.198       0.0021       0.0042
MSA_non.exonic_Ovr                               141673         130217       0.112        0.2595        0.2966      -0.287       0.0223      0.03964


(Postscript version of above)