Annotation results

Affy RNA (thresh)/H3ac/H3K27me3/TR50 (wavelet) 4-track, 2-state segmentation

Number of segments State 0: 62 State 1: 53 Total size (bp) State 0: 16320938 State 1: 12936947 Avg. segment length State 0: 263241 State 1: 244093 Median segment length State 0: 188999 State 1: 130999 Minimum segment length State 0: 16999 State 1: 27999 Maximum segment length State 0: 1117999 State 1: 1094999

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                                588 (0.217)           2121 (0.783)      -0.611            0            0       0.771            0            0
Num_mRNA_TxStarts                                   917 (0.199)           3698 (0.801)      -0.644            0            0       0.812            0            0
Num_Spliced.EST_TxStarts                          15189 (0.116)         115531 (0.884)      -0.792       0.0001    0.0002833       0.999       0.0014     0.003173
EST_Ovr                                         9250097 (0.486)        9776837 (0.514)      -0.128       0.0027     0.005738       0.162       0.0004    0.0009714
CpG.UCSC_Isl_Ovr                                  69104 (0.183)         308325 (0.817)      -0.672            0            0       0.848            0            0
RptMskr_Ovr                                     7266816 (0.550)        5952407 (0.450)      -0.015       0.1973       0.2033       0.018       0.1854        0.197
RptMskr_DNA_Ovr                                  491817 (0.605)         320946 (0.395)       0.085       0.0237      0.03152      -0.107       0.0149      0.02303
RptMskr_LINE.L1_Ovr                             2718900 (0.663)        1379214 (0.337)       0.189       0.0003    0.0007846      -0.239            0            0
RptMskr_LINE.L2_Ovr                              596075 (0.597)         402723 (0.403)       0.070       0.0558      0.06324      -0.088       0.0452      0.05299
RptMskr_LTR_Ovr                                 1354800 (0.659)         700604 (0.341)       0.182            0            0      -0.229            0            0
RptMskr_SINE.ALU_Ovr                            1247416 (0.329)        2538678 (0.671)      -0.409            0            0       0.516            0            0
SimpRep_Ovr                                      298957 (0.433)         391776 (0.567)      -0.224       0.0034       0.0068       0.283       0.0063       0.0119
MSA_strict_Ovr                                   332652 (0.466)         381347 (0.534)      -0.165       0.0283      0.03564       0.208       0.0197      0.02912
MSA_moderate_Ovr                                 706557 (0.483)         756471 (0.517)      -0.134       0.0241      0.03152       0.169       0.0141      0.02303
MSA_loose_Ovr                                   1757850 (0.504)        1726910 (0.496)      -0.096       0.0143      0.02303       0.121       0.0082      0.01467
MSA_non.exonic_Ovr                               589993 (0.660)         303737 (0.340)       0.183       0.0351      0.04262      -0.231       0.0226      0.03152
DiseaseVarMerge_Ovr                                1212 (0.399)           1824 (0.601)      -0.284       0.2082       0.2082       0.359       0.1821        0.197

(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                        1911479.69        23768.5
Gencode_3P_Dist_Known                        1910958.24        22697.5
Gencode_5P_Dist_Putative                     4329858.51       115669.0
Gencode_3P_Dist_Putative                     4327609.53       110312.5
Gencode_5P_Dist_Pseudo                       1478486.84        81615.5
Gencode_3P_Dist_Pseudo                       1478777.27        81679.5
Gencode_TxStop_Dist                           471560.71        15029.5
Gencode_TxStart_Dist                          472376.85        13816.0
Gencode_5P.UTR_Dist                          1925304.37        23836.0
Gencode_1stExon_Dist                          473262.01        14053.0
KnownGene_3P_Dist                              99146.67        36865.5
KnownGene_5P_Dist                              96453.33        32251.5
Ensemble_5P_Dist                               91520.14        28983.0
Refseq_5P_Dist                                105259.25        42114.0
mRNA_5P_Dist                                   59533.27        18263.5
mRNA_3P_Dist                                   55443.50        23271.0
Spliced.EST_5P_Dist                            17806.71         4652.5
Spliced.EST_3P_Dist                            15657.89         4039.5
CpG.UCSC_Isl_Dist                             116386.75        42854.5
CpG.AL_Isl_Dist                               906178.89        23854.5
Nhgri_Chip.GM_Dist                            878566.26        14467.0
UWDHS.CAP.GM_Dist                             874890.52        17646.5
UWDHS.QCP.GM_Dist                           23446267.35      1955513.0
UWDHS.QCP.HeLa_Dist                         23437956.87      1932809.0
UVaDnaRep.OriginsPred_Dist                     54317.52        39059.5
Sanger_ChipCenters.H3K4me1.GM_Dist             26907.04         8474.5
Sanger_ChipCenters.H3K4me1.HeLa_Dist          496813.57        16009.5
Sanger_ChipCenters.H3K4me2.GM_Dist             33286.54        11724.0
Sanger_ChipCenters.H3K4me2.HeLa_Dist         2935330.65        39048.0
Sanger_ChipCenters.H3K4me3.GM_Dist             48611.17        22672.5
Sanger_ChipCenters.H3K4me3.HeLa_Dist         3792239.72        38965.0
Sanger_ChipCenters.H3ac.GM_Dist                74392.13        31095.0
Sanger_ChipCenters.H3ac.HeLa_Dist            2509346.08        55519.5
Sanger_ChipCenters.H4ac.GM_Dist                62035.71        25163.0
Sanger_ChipCenters.H4ac.HeLa_Dist            1517214.66        41877.0
Uva_DnaRep.Early_Dist                       11847833.77       123623.5
Uva_DnaRep.Mid_Dist                          6877780.21        48435.5
Uva_DnaRep.Late_Dist                          526025.85        58807.5
Uva_DnaRep.PanS_Dist                         5432561.62       154897.0
MSA_non.exonic_Dist                            11357.17        10259.0