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|name=uterus, adult
|name=uterus, adult
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Revision as of 12:22, 18 June 2014


Name:uterus, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10509
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueuterus
dev stageadult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008992
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10509 CAGE DRX009129 DRR010003
Accession ID Mm9

Library idBAMCTSS
CNhs10509 DRZ001428 DRZ002811
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10509

00
10
100
1000
10000.0564
10010.147
1002-0.0624
10030.197
10040.737
10050.137
10060
10070.041
10080
10090.328
1010.0583
10100
10110
10120
10130.0847
1014-0.0874
1015-0.0662
10160.038
10170
10180.19
10190
1020
10200
1021-0.0487
10220.0583
10230
10240.0847
10250.0294
10260.0436
1027-0.0163
10280.073
10290.247
1030.269
10300
10310.425
1032-0.103
10330
10340.073
10350
10360.00733
10370
10380.0237
1039-0.11
1040
10400.108
10410.136



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10509

Jaspar motifP-value
MA0002.20.234
MA0003.10.0525
MA0004.10.645
MA0006.10.0633
MA0007.10.494
MA0009.10.219
MA0014.10.898
MA0017.10.00572
MA0018.20.0301
MA0019.10.275
MA0024.13.88638e-4
MA0025.10.585
MA0027.10.109
MA0028.10.0317
MA0029.10.127
MA0030.10.234
MA0031.10.118
MA0035.22.18553e-4
MA0038.10.802
MA0039.20.0103
MA0040.10.561
MA0041.10.36
MA0042.10.429
MA0043.10.0297
MA0046.10.72
MA0047.20.344
MA0048.10.699
MA0050.12.59579e-15
MA0051.17.4444e-9
MA0052.10.476
MA0055.10.318
MA0057.10.645
MA0058.10.544
MA0059.10.134
MA0060.11.35348e-8
MA0061.10.0661
MA0062.20.11
MA0065.20.136
MA0066.10.116
MA0067.10.566
MA0068.10.779
MA0069.10.314
MA0070.10.614
MA0071.10.13
MA0072.10.919
MA0073.10.792
MA0074.10.674
MA0076.10.0305
MA0077.10.532
MA0078.10.0383
MA0079.20.0197
MA0080.21.87407e-6
MA0081.10.66
MA0083.13.30071e-4
MA0084.10.267
MA0087.10.293
MA0088.10.638
MA0090.10.0994
MA0091.10.128
MA0092.10.914
MA0093.10.657
MA0099.21.44974e-9
MA0100.10.15
MA0101.10.00784
MA0102.20.816
MA0103.10.18
MA0104.20.0431
MA0105.10.724
MA0106.10.584
MA0107.18.21536e-4
MA0108.20.811
MA0111.10.493
MA0112.20.0191
MA0113.10.975
MA0114.10.00115
MA0115.10.00109
MA0116.10.588
MA0117.10.462
MA0119.10.312
MA0122.10.712
MA0124.10.917
MA0125.10.00982
MA0131.10.17
MA0135.10.573
MA0136.11.09973e-4
MA0137.20.00138
MA0138.20.714
MA0139.10.566
MA0140.15.53801e-4
MA0141.12.97999e-5
MA0142.10.345
MA0143.10.251
MA0144.14.86885e-4
MA0145.10.00313
MA0146.10.802
MA0147.10.0272
MA0148.10.542
MA0149.10.175
MA0150.10.381
MA0152.10.128
MA0153.10.0599
MA0154.10.304
MA0155.10.8
MA0156.11.24072e-5
MA0157.10.0274
MA0159.10.176
MA0160.10.0146
MA0162.10.53
MA0163.10.681
MA0164.10.457
MA0258.10.265
MA0259.10.0962



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10509

Novel motifP-value
10.399
100.184
1000.0372
1010.73
1020.364
1030.712
1040.163
1050.391
1060.00157
1070.0181
1080.619
1090.334
110.309
1100.718
1110.52
1120.222
1130.524
1140.258
1150.634
1160.939
1170.00702
1180.0505
1190.612
120.98
1200.258
1210.221
1220.737
1230.222
1240.692
1250.447
1260.355
1270.139
1280.0611
1290.291
130.107
1300.0639
1310.605
1320.842
1330.31
1340.419
1350.895
1360.458
1370.12
1380.0665
1390.729
140.715
1400.0538
1410.984
1420.441
1430.373
1440.936
1450.356
1460.273
1470.0865
1480.171
1490.139
150.283
1500.524
1510.909
1520.0192
1530.341
1540.798
1550.484
1563.97782e-4
1570.727
1580.623
1590.166
1600.434
1610.564
1620.87
1630.963
1640.911
1650.961
1660.00112
1670.201
1680.382
1690.0261
170.386
180.0797
190.00676
20.00759
200.203
210.497
220.194
230.373
240.175
250.281
260.0688
270.347
280.751
290.406
30.855
300.178
310.805
320.589
330.614
340.769
350.0648
360.0404
370.385
380.731
390.467
40.903
400.445
410.175
420.807
430.764
440.26
450.0867
460.459
470.867
480.671
490.923
50.704
500.264
510.867
520.0686
530.102
540.962
550.757
560.969
570.179
580.817
590.393
60.303
600.184
610.22
620.622
630.493
640.303
650.96
660.292
670.718
680.862
690.243
70.945
700.939
710.541
720.623
730.297
740.462
750.317
760.0928
770.608
780.391
790.733
80.0707
800.0608
810.936
820.696
830.958
840.742
850.491
860.641
870.562
880.834
890.537
90.24
900.0461
910.459
920.383
930.274
940.398
950.436
960.0467
970.464
980.884
990.32



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10509


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000995 (uterus)
0003134 (female reproductive organ)
0000479 (tissue)
0005156 (reproductive structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011440 (mouse uterus- adult sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005795 (embryonic uterus)
UBERON:0010316 (germ layer / neural crest)

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