Annotation results

Uva TR50 data, HeLa, 2-state segmentation (state 0 = active!)

Number of segments State 0: 48 State 1: 46 Total size (bp) State 0: 16697602 State 1: 12152304 Avg. segment length State 0: 347867 State 1: 264181 Median segment length State 0: 334499 State 1: 180349 Minimum segment length State 0: 6699 State 1: 4499 Maximum segment length State 0: 1617849 State 1: 746949

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                               2050 (0.766)            626 (0.234)       0.324       0.0062      0.01804      -0.445       0.0005       0.0032
Num_mRNA_TxStarts                                  3643 (0.794)            944 (0.206)       0.372       0.0414      0.06309      -0.511       0.0036       0.0128
Num_Spliced.EST_TxStarts                         113086 (0.867)          17421 (0.133)       0.497       0.2131         0.31      -0.683       0.0143      0.02805
EST_Ovr                                        11753917 (0.629)        6940103 (0.371)       0.086       0.0383      0.06309      -0.119       0.0149      0.02805
CpG.UCSC_Isl_Ovr                                 290627 (0.788)          78423 (0.212)       0.361       0.0103      0.02354      -0.496       0.0002     0.002133
RptMskr_Ovr                                     7603009 (0.585)        5399303 (0.415)       0.010       0.2874       0.3679      -0.014       0.2293        0.319
RptMskr_DNA_Ovr                                  466531 (0.581)         336239 (0.419)       0.004       0.4631       0.4631      -0.006       0.4525       0.4631
RptMskr_LINE.L1_Ovr                             2033172 (0.502)        2014051 (0.498)      -0.132       0.0089      0.02191       0.181        0.001     0.005333
RptMskr_LINE.L2_Ovr                              561846 (0.574)         417754 (0.426)      -0.009        0.434       0.4629       0.012       0.4134       0.4629
RptMskr_LTR_Ovr                                 1003425 (0.497)        1014096 (0.503)      -0.141       0.0016       0.0064       0.193       0.0001       0.0016
RptMskr_SINE.ALU_Ovr                            2763642 (0.744)         950773 (0.256)       0.286       0.0005       0.0032      -0.392            0            0
SimpRep_Ovr                                      357587 (0.533)         313838 (0.467)      -0.080        0.314       0.3865       0.110       0.2523       0.3364
MSA_strict_Ovr                                   473982 (0.666)         237857 (0.334)       0.150       0.0409      0.06309      -0.207       0.0084      0.02191
MSA_moderate_Ovr                                 953775 (0.656)         500792 (0.344)       0.133       0.0288       0.0512      -0.183       0.0059      0.01804
MSA_loose_Ovr                                   2201836 (0.638)        1250368 (0.362)       0.102       0.0145      0.02805      -0.140       0.0015       0.0064
MSA_non.exonic_Ovr                               505808 (0.567)         385591 (0.433)      -0.020       0.4246       0.4629       0.027       0.4021       0.4629

(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                        2532759.42        20406.0
Gencode_3P_Dist_Known                        2531035.48        26590.0
Gencode_5P_Dist_Putative                     3816149.75       138842.0
Gencode_3P_Dist_Putative                     3814031.28       143266.0
Gencode_5P_Dist_Pseudo                       2240602.19       121504.0
Gencode_3P_Dist_Pseudo                       2240426.35       112402.0
Gencode_TxStop_Dist                           545913.72        12385.0
Gencode_TxStart_Dist                          548619.48        11939.0
Gencode_5P.UTR_Dist                          2545128.63        24432.0
Gencode_1stExon_Dist                          549677.47        14346.0
KnownGene_3P_Dist                             119788.64        45832.0
KnownGene_5P_Dist                             116283.13        39022.0
Ensemble_5P_Dist                              114109.74        42397.0
Refseq_5P_Dist                                120900.47        47690.0
mRNA_5P_Dist                                   66462.40        19803.0
mRNA_3P_Dist                                   64984.62        25107.0
Spliced.EST_5P_Dist                            18988.01         4476.0
Spliced.EST_3P_Dist                            16486.99         3108.0
CpG.UCSC_Isl_Dist                             144064.36        57745.0
CpG.AL_Isl_Dist                              1058199.51        27165.0
Nhgri_Chip.GM_Dist                           1013955.15        17557.0
UWDHS.CAP.GM_Dist                             633119.45        23673.0
UWDHS.QCP.GM_Dist                           21250180.09       956447.0
UWDHS.QCP.HeLa_Dist                         21241171.03       933743.0
UVaDnaRep.OriginsPred_Dist                     61024.95        49197.0
Sanger_ChipCenters.H3K4me1.GM_Dist             30649.32        14590.0
Sanger_ChipCenters.H3K4me1.HeLa_Dist          579849.69        30001.0
Sanger_ChipCenters.H3K4me2.GM_Dist             39441.23        18589.0
Sanger_ChipCenters.H3K4me2.HeLa_Dist         3357107.73        65098.0
Sanger_ChipCenters.H3K4me3.GM_Dist             54383.19        26985.0
Sanger_ChipCenters.H3K4me3.HeLa_Dist         4874746.61        62894.0
Sanger_ChipCenters.H3ac.GM_Dist                81246.82        46538.0
Sanger_ChipCenters.H3ac.HeLa_Dist            3760385.10        84958.0
Sanger_ChipCenters.H4ac.GM_Dist                70065.26        44899.0
Sanger_ChipCenters.H4ac.HeLa_Dist            2097119.84        81286.0
Uva_DnaRep.Early_Dist                        9926312.06       149191.5
Uva_DnaRep.Mid_Dist                          4089138.76        19698.0
Uva_DnaRep.Late_Dist                          765624.61        17349.0
Uva_DnaRep.PanS_Dist                         5509666.08       159074.0
MSA_non.exonic_Dist                             9165.43         3329.0