Annotation results

UCSD Chip data, H3K27me3, HeLa, 64kb wavelet smooth data, 2-state segmentation (state 0 = active!)

Number of segments State 0: 59 State 1: 50 Total size (bp) State 0: 18907441 State 1: 10964950 Avg. segment length State 0: 320465 State 1: 219299 Median segment length State 0: 305499 State 1: 152249 Minimum segment length State 0: 16999 State 1: 16999 Maximum segment length State 0: 1610499 State 1: 661999

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                               1889 (0.666)            946 (0.334)       0.053       0.3129       0.4397      -0.091       0.2318       0.4035
Num_mRNA_TxStarts                                  3350 (0.693)           1486 (0.307)       0.094       0.4272       0.4882      -0.163       0.3474       0.4447
Num_Spliced.EST_TxStarts                         106252 (0.768)          32161 (0.232)       0.213       0.5211       0.5211      -0.367       0.4522        0.499
EST_Ovr                                        12753321 (0.655)        6717104 (0.345)       0.035       0.2094       0.3942      -0.060       0.1265       0.3488
CpG.UCSC_Isl_Ovr                                 236210 (0.598)         158645 (0.402)      -0.055        0.316       0.4397       0.095       0.2492       0.4035
RptMskr_Ovr                                     8487845 (0.633)        4930580 (0.367)      -0.001       0.4875       0.5032       0.001       0.4814       0.5032
RptMskr_DNA_Ovr                                  506652 (0.616)         316189 (0.384)      -0.027       0.2648       0.4035       0.047       0.1709       0.3765
RptMskr_LINE.L1_Ovr                             2515460 (0.603)        1654275 (0.397)      -0.047       0.1765       0.3765       0.081       0.0882       0.3488
RptMskr_LINE.L2_Ovr                              624311 (0.621)         381479 (0.379)      -0.019       0.3318       0.4424       0.033       0.2535       0.4035
RptMskr_LTR_Ovr                                 1204560 (0.575)         888942 (0.425)      -0.091       0.0235       0.2376       0.157       0.0035       0.0928
RptMskr_SINE.ALU_Ovr                            2753899 (0.720)        1072386 (0.280)       0.137       0.0478       0.3059      -0.236       0.0058       0.0928
SimpRep_Ovr                                      425392 (0.567)         324902 (0.433)      -0.104       0.1308       0.3488       0.180       0.0599       0.3195
MSA_strict_Ovr                                   487143 (0.680)         229583 (0.320)       0.074       0.1985       0.3942      -0.127       0.1101       0.3488
MSA_moderate_Ovr                                 995921 (0.674)         481694 (0.326)       0.065       0.1696       0.3765      -0.112       0.0795       0.3488
MSA_loose_Ovr                                   2363584 (0.669)        1167535 (0.331)       0.058       0.0984       0.3488      -0.099       0.0297       0.2376
MSA_non.exonic_Ovr                               585635 (0.651)         314512 (0.349)       0.028       0.4168       0.4882      -0.048       0.3752       0.4618

(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                        2193847.73        18111.0
Gencode_3P_Dist_Known                        2193299.37        13505.0
Gencode_5P_Dist_Putative                     3594748.04       109883.0
Gencode_3P_Dist_Putative                     3593198.26       105084.0
Gencode_5P_Dist_Pseudo                       1497712.19        91153.0
Gencode_3P_Dist_Pseudo                       1497532.63        91679.0
Gencode_TxStop_Dist                           709834.90         7566.0
Gencode_TxStart_Dist                          712393.16         8503.0
Gencode_5P.UTR_Dist                          2209526.81        17996.0
Gencode_1stExon_Dist                          713330.50         9109.0
KnownGene_3P_Dist                             103287.55        33326.0
KnownGene_5P_Dist                              99666.19        31195.0
Ensemble_5P_Dist                               99652.51        29769.0
Refseq_5P_Dist                                104971.19        41552.0
mRNA_5P_Dist                                   57949.16        14214.0
mRNA_3P_Dist                                   54734.16        17112.0
Spliced.EST_5P_Dist                            19647.92         4200.0
Spliced.EST_3P_Dist                            16357.48         2731.0
CpG.UCSC_Isl_Dist                             121213.92        48149.0
CpG.AL_Isl_Dist                               945638.61        21188.0
Nhgri_Chip.GM_Dist                            905049.95        13636.0
UWDHS.CAP.GM_Dist                             568795.80        16056.0
UWDHS.QCP.GM_Dist                           21166098.82        93704.0
UWDHS.QCP.HeLa_Dist                         21158805.30        85196.0
UVaDnaRep.OriginsPred_Dist                    178666.07        41023.0
Sanger_ChipCenters.H3K4me1.GM_Dist             26982.22        10785.0
Sanger_ChipCenters.H3K4me1.HeLa_Dist          744807.54        14196.0
Sanger_ChipCenters.H3K4me2.GM_Dist             35214.76        12973.0
Sanger_ChipCenters.H3K4me2.HeLa_Dist         3101991.00        38553.0
Sanger_ChipCenters.H3K4me3.GM_Dist             47537.49        17632.0
Sanger_ChipCenters.H3K4me3.HeLa_Dist         3756224.31        32436.0
Sanger_ChipCenters.H3ac.GM_Dist                78071.71        30885.0
Sanger_ChipCenters.H3ac.HeLa_Dist            2510037.72        58002.0
Sanger_ChipCenters.H4ac.GM_Dist                64845.82        26826.0
Sanger_ChipCenters.H4ac.HeLa_Dist            1569454.23        51666.0
Uva_DnaRep.Early_Dist                       11101354.53       142697.0
Uva_DnaRep.Mid_Dist                          5537731.89        56930.0
Uva_DnaRep.Late_Dist                         1076867.67        68135.0
Uva_DnaRep.PanS_Dist                         5357751.44       151935.0
MSA_non.exonic_Dist                             9380.50         6908.5