Annotation results

H3ac/H3K27me3/TR50 (wavelet) 3-track, 2-state segmentation

Number of segments State 0: 48 State 1: 52 Total size (bp) State 0: 14497952 State 1: 14759948 Avg. segment length State 0: 302041 State 1: 283845 Median segment length State 0: 199999 State 1: 230999 Minimum segment length State 0: 999 State 1: 21999 Maximum segment length State 0: 1593999 State 1: 1160999

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                               1871 (0.691)            838 (0.309)       0.394       0.0014     0.005564      -0.387       0.0001      0.00085
Num_mRNA_TxStarts                                  3310 (0.717)           1305 (0.283)       0.447       0.0197       0.0319      -0.439       0.0059      0.01254
Num_Spliced.EST_TxStarts                         108245 (0.828)          22476 (0.172)       0.671       0.0785       0.1213      -0.659       0.0119      0.02023
EST_Ovr                                        10742157 (0.565)        8284782 (0.435)       0.139       0.0017     0.005564      -0.137       0.0026     0.005893
CpG.UCSC_Isl_Ovr                                 254343 (0.674)         123085 (0.326)       0.360       0.0106      0.01897      -0.354       0.0025     0.005893
RptMskr_Ovr                                     6526095 (0.494)        6693133 (0.506)      -0.004       0.4241       0.4791       0.004       0.4201       0.4791
RptMskr_DNA_Ovr                                  382608 (0.471)         430155 (0.529)      -0.050       0.1533       0.2172       0.049       0.1381       0.2041
RptMskr_LINE.L1_Ovr                             1693052 (0.413)        2405066 (0.587)      -0.166       0.0022     0.005893       0.163       0.0006       0.0034
RptMskr_LINE.L2_Ovr                              479687 (0.480)         519108 (0.520)      -0.031       0.2875        0.376       0.030       0.2711       0.3687
RptMskr_LTR_Ovr                                  790152 (0.384)        1265254 (0.616)      -0.224            0            0       0.220            0            0
RptMskr_SINE.ALU_Ovr                            2510229 (0.663)        1275867 (0.337)       0.338       0.0006       0.0034      -0.332       0.0001      0.00085
SimpRep_Ovr                                      332051 (0.481)         358683 (0.519)      -0.030       0.4105       0.4791       0.029       0.4044       0.4791
MSA_strict_Ovr                                   433991 (0.608)         280008 (0.392)       0.227       0.0067      0.01266      -0.223       0.0017     0.005564
MSA_moderate_Ovr                                 857715 (0.586)         605314 (0.414)       0.183       0.0064      0.01266      -0.180       0.0025     0.005893
MSA_loose_Ovr                                   1963768 (0.564)        1520991 (0.436)       0.137       0.0018     0.005564      -0.135       0.0013     0.005564
MSA_non.exonic_Ovr                               437334 (0.489)         456398 (0.511)      -0.012       0.4509       0.4791       0.012       0.4472       0.4791
DiseaseVarMerge_Ovr                                1509 (0.497)           1527 (0.503)       0.003       0.4995       0.4995      -0.003       0.4992       0.4995

(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                        2108304.45        21254.0
Gencode_3P_Dist_Known                        2111493.90        17569.0
Gencode_5P_Dist_Putative                     3480968.34       120345.0
Gencode_3P_Dist_Putative                     3477983.81       113889.0
Gencode_5P_Dist_Pseudo                       2126153.46        90401.5
Gencode_3P_Dist_Pseudo                       2125905.88        89192.0
Gencode_TxStop_Dist                           523102.66         9903.0
Gencode_TxStart_Dist                          523503.15        12311.0
Gencode_5P.UTR_Dist                          2122968.08        20886.0
Gencode_1stExon_Dist                          524533.71        12649.0
KnownGene_3P_Dist                             111130.80        44986.0
KnownGene_5P_Dist                             107600.47        38440.0
Ensemble_5P_Dist                              107678.10        37076.0
Refseq_5P_Dist                                112562.63        46558.0
mRNA_5P_Dist                                   61144.80        15865.0
mRNA_3P_Dist                                   59572.46        20621.0
Spliced.EST_5P_Dist                            19077.55         3646.0
Spliced.EST_3P_Dist                            16886.35         3075.0
CpG.UCSC_Isl_Dist                             120808.87        52009.0
CpG.AL_Isl_Dist                              1005883.57        26530.0
Nhgri_Chip.GM_Dist                            973069.99        17000.0
UWDHS.CAP.GM_Dist                             603812.09        15081.0
UWDHS.QCP.GM_Dist                           19565438.41        93544.0
UWDHS.QCP.HeLa_Dist                         19559723.36        92843.0
UVaDnaRep.OriginsPred_Dist                     58210.67        47488.0
Sanger_ChipCenters.H3K4me1.GM_Dist             27162.46         9990.0
Sanger_ChipCenters.H3K4me1.HeLa_Dist          559906.57        16447.0
Sanger_ChipCenters.H3K4me2.GM_Dist             34785.34        12139.0
Sanger_ChipCenters.H3K4me2.HeLa_Dist         2885844.57        45773.0
Sanger_ChipCenters.H3K4me3.GM_Dist             52796.96        22904.0
Sanger_ChipCenters.H3K4me3.HeLa_Dist         4330830.01        40866.0
Sanger_ChipCenters.H3ac.GM_Dist                75250.46        37461.0
Sanger_ChipCenters.H3ac.HeLa_Dist            3439247.53        69455.0
Sanger_ChipCenters.H4ac.GM_Dist                61364.80        25661.0
Sanger_ChipCenters.H4ac.HeLa_Dist            1678093.57        53623.0
Uva_DnaRep.Early_Dist                       10858099.80       103774.5
Uva_DnaRep.Mid_Dist                          5417048.30        33196.0
Uva_DnaRep.Late_Dist                         1129005.12        65124.0
Uva_DnaRep.PanS_Dist                         6568766.84       172196.5
MSA_non.exonic_Dist                            10243.67         6974.0