High-confidence active/inactive segments

Following are segments whose state assignments agree across all 6different segmentations.

1. one-track segmentation of 64kb wavelet-smoothed Sanger H4ac
2. one-track segmentation of 64kb wavelet-smoothed UCSD H3K27me3
3. one-track segmentation of 64kb wavelet-smoothed MSA non-exonic, 3kb sliding window
4. one-track segmentation of TR50
5. five-track segmentation of all of the above, plus Affy RNA

Specifically, coordinates of the "Active" segments below fell in state 1 for the five-track and H4ac segmentations, and in state 0 for H3K27me3, MSA, and TR50. Coordinates of the "Inactive" segments fell in state 0 for the five-track, H4ac, and Affy segmenations, and in state 1 for H3K27me3, MSA, and TR50.

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

Active/Inactive segment statistics

• Number of segments
• Inactive: 25
• Active: 50
• Total size (bp)
• Inactive: 2236142
• Active: 4775633
• Avg. segment length
• Inactive: 89446
• Active: 95513
• Median segment length
• Inactive: 57249
• Active: 70387.5
• Minimum segment length
• Inactive: 9817
• Active: 1174
• Maximum segment length
• Inactive: 230649
• 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                                 32            988      -0.849             0             0       1.187            0            0
Num_mRNA_TxStarts                                    17           2262      -0.953             0             0       1.936            0            0
Num_Spliced.EST_TxStarts                            297          89524      -0.971             0             0       3.061            0            0
EST_Ovr                                         1468423        3836038       0.007        0.4652        0.4827       0.232       0.0001    0.0002133
CpG.UCSC_Isl_Ovr                                   4813         124376      -0.837             0             0       0.977            0            0
RptMskr_Ovr                                      957791        2250056      -0.050        0.0779        0.1187       0.045       0.0526      0.08859
RptMskr_DNA_Ovr                                   69611          99499       0.131        0.0603       0.09648      -0.243            0            0
RptMskr_LINE.L1_Ovr                              311893         406427      -0.009        0.4676        0.4827      -0.395            0            0
RptMskr_LINE.L2_Ovr                              101058         140876       0.345             0             0      -0.122       0.0484      0.08604
RptMskr_LTR_Ovr                                  174554         211012       0.106        0.1087        0.1512      -0.374            0            0
RptMskr_SINE.ALU_Ovr                             148407        1177535      -0.482        0.0004        0.0008       0.923            0            0
SimpRep_Ovr                                       39793         143100      -0.291        0.1351        0.1717       0.194       0.1755        0.208
MSA_strict_Ovr                                    64084         121928       0.199        0.1395        0.1717       0.068       0.3088       0.3529
MSA_moderate_Ovr                                 131931         244526       0.197        0.0926        0.1347       0.039        0.352       0.3884
MSA_loose_Ovr                                    293720         563551       0.114        0.1176        0.1568       0.001       0.4874       0.4874
MSA_non.exonic_Ovr                               125614          58388       0.871        0.0005     0.0009412      -0.593            0            0


(Postscript version of above)