Annotation results

Affy RNA (thresh)/H3ac/H3K27me3/MSA/TR50 (wavelet) 5-track, 2-state segmentation

Number of segments State 0: 61 State 1: 53 Total size (bp) State 0: 16334939 State 1: 12922947 Avg. segment length State 0: 267786 State 1: 243829 Median segment length State 0: 175999 State 1: 140999 Minimum segment length State 0: 16999 State 1: 3999 Maximum segment length State 0: 1116999 State 1: 1099999

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 KnownGene Overlap with state0 Overlap with state1 Gencode.Known Overlap with state0 Overlap with state1 Ensembl Overlap with state0 GO term analysis -- biological process GO term analysis -- molecular function GO term analysis -- cellular components Overlap with state1 GO term analysis -- biological process GO term analysis -- molecular function GO term analysis -- cellular components

Enrichment of various elements

Total number of bases or elements overlapping each state. Numbers in parentheses are the fractions of the element in that state. Second set of columns gives enrichment over expected (as a fraction). Enrichment p-values, computed by permuting state labels on the fixed segmentation, are also included, with adjusted p-values using method "BH".

Element                                                     st0                    st1     st0 enr    st0 enr p    st0 adj p     st1 enr    st1 enr p    st1 adj p
-------------------------                  --------------------   --------------------   ---------   ----------   ----------   ---------   ----------   ----------
Num_Gencode_TxStarts                                582 (0.215)           2127 (0.785)      -0.615            0            0       0.778            0            0
Num_mRNA_TxStarts                                   905 (0.196)           3710 (0.804)      -0.649            0            0       0.820            0            0
Num_Spliced.EST_TxStarts                          15386 (0.118)         115334 (0.882)      -0.789       0.0002    0.0005818       0.998       0.0002    0.0005818
EST_Ovr                                         9286375 (0.488)        9740560 (0.512)      -0.126        0.003        0.006       0.159       0.0006      0.00128
CpG.UCSC_Isl_Ovr                                  70669 (0.187)         306758 (0.813)      -0.665            0            0       0.840            0            0
RptMskr_Ovr                                     7226249 (0.547)        5992974 (0.453)      -0.021        0.112        0.112       0.026       0.0965      0.09961
RptMskr_DNA_Ovr                                  486621 (0.599)         326141 (0.401)       0.072       0.0495      0.06092      -0.092       0.0299      0.04349
RptMskr_LINE.L1_Ovr                             2693944 (0.657)        1404172 (0.343)       0.177       0.0003    0.0007385      -0.224       0.0003    0.0007385
RptMskr_LINE.L2_Ovr                              594843 (0.596)         403953 (0.404)       0.067       0.0695      0.07413      -0.084       0.0583       0.0691
RptMskr_LTR_Ovr                                 1343976 (0.654)         711430 (0.346)       0.171       0.0005     0.001143      -0.216       0.0001    0.0003556
RptMskr_SINE.ALU_Ovr                            1245502 (0.329)        2540590 (0.671)      -0.411            0            0       0.519            0            0
SimpRep_Ovr                                      298001 (0.431)         392732 (0.569)      -0.227       0.0034       0.0064       0.287       0.0045        0.008
MSA_strict_Ovr                                   345332 (0.484)         368664 (0.516)      -0.134       0.0654      0.07217       0.169       0.0456      0.05837
MSA_moderate_Ovr                                 730247 (0.499)         732779 (0.501)      -0.106       0.0653      0.07217       0.134       0.0422      0.05627
MSA_loose_Ovr                                   1789584 (0.514)        1695177 (0.486)      -0.080       0.0367      0.05106       0.101       0.0219      0.03337
MSA_non.exonic_Ovr                               606933 (0.679)         286796 (0.321)       0.216       0.0137      0.02192      -0.273       0.0067      0.01128

(Postscript version of above)

Distances of elements to segment boundaries

Results for each boundary

Average and median absolute value over all boundaries.

Statistic                                      avg(|d|)       med(|d|)
-------------------------                  ------------   ------------
Gencode_5P_Dist_Known                        1923330.38        23218.0
Gencode_3P_Dist_Known                        1923271.69        23983.0
Gencode_5P_Dist_Putative                     4115089.40       119865.0
Gencode_3P_Dist_Putative                     4112723.87       111153.0
Gencode_5P_Dist_Pseudo                       1487451.61        87961.0
Gencode_3P_Dist_Pseudo                       1487708.73        87423.0
Gencode_TxStop_Dist                           474805.85        14556.0
Gencode_TxStart_Dist                          475366.55        14275.0
Gencode_5P.UTR_Dist                          1937114.34        22818.0
Gencode_1stExon_Dist                          476270.48        14979.0
KnownGene_3P_Dist                             100574.90        44855.0
KnownGene_5P_Dist                              97115.21        33185.0
Ensemble_5P_Dist                               91878.41        30058.0
Refseq_5P_Dist                                105982.16        42403.0
mRNA_5P_Dist                                   59924.59        17043.0
mRNA_3P_Dist                                   55954.10        23729.0
Spliced.EST_5P_Dist                            18085.27         4636.0
Spliced.EST_3P_Dist                            15618.02         3886.0
CpG.UCSC_Isl_Dist                             116585.97        45514.0
CpG.AL_Isl_Dist                               912490.95        25627.0
Nhgri_Chip.GM_Dist                            884161.34        14454.0
UWDHS.CAP.GM_Dist                             880372.15        18243.0
UWDHS.QCP.GM_Dist                           23325744.07      1456513.5
UWDHS.QCP.HeLa_Dist                         23317119.57      1433809.5
UVaDnaRep.OriginsPred_Dist                     55974.82        41250.0
Sanger_ChipCenters.H3K4me1.GM_Dist             27478.26        11032.0
Sanger_ChipCenters.H3K4me1.HeLa_Dist          499710.60        16371.0
Sanger_ChipCenters.H3K4me2.GM_Dist             33826.48        12700.0
Sanger_ChipCenters.H3K4me2.HeLa_Dist         2954071.06        38472.0
Sanger_ChipCenters.H3K4me3.GM_Dist             49760.41        23939.0
Sanger_ChipCenters.H3K4me3.HeLa_Dist         3817241.57        38472.0
Sanger_ChipCenters.H3ac.GM_Dist                74078.55        30550.0
Sanger_ChipCenters.H3ac.HeLa_Dist            2524591.29        51548.0
Sanger_ChipCenters.H4ac.GM_Dist                63982.37        27435.0
Sanger_ChipCenters.H4ac.HeLa_Dist            1527359.45        42057.0
Uva_DnaRep.Early_Dist                       11935006.28       129001.0
Uva_DnaRep.Mid_Dist                          6924886.20        52820.0
Uva_DnaRep.Late_Dist                          534822.72        57762.0
Uva_DnaRep.PanS_Dist                         5475506.53       152521.5
MSA_non.exonic_Dist                            10583.50         7759.0