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|library_id=CNhs10507
|library_id=CNhs10507
|library_id_phase_based=2:CNhs10507
|library_id_phase_based=2:CNhs10507
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;91
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;91
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/ovary%252c%2520adult.CNhs10507.91-2I7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/ovary%252c%2520adult.CNhs10507.91-2I7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/ovary%252c%2520adult.CNhs10507.91-2I7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/ovary%252c%2520adult.CNhs10507.91-2I7.mm10.nobarcode.ctss.bed.gz

Revision as of 22:38, 18 May 2017


Name:ovary, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10507
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueovary
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  SAMD00005245
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10507 CAGE DRX009050 DRR009924
Accession ID Mm9

Library idBAMCTSS
CNhs10507 DRZ001349 DRZ002732
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10507

00
10
100
1000
10000.0576
10010.0957
10020.0994
10030.149
10040.974
10050
10060.0119
10070.0232
10080
10090.325
1010.0362
10100
10110.0576
10120
10130.0652
1014-0.0275
1015-0.0815
10160.0326
10170
10180
10190
1020
10200
10210
10220.351
10230
10240.168
10250.0576
10260
10270
10280.109
10290.0184
1030.0576
10300
10310.249
10320.091
10330.0576
10340.0576
10350.0576
1036-0.106
10370
10380.0561
10390.153
1040
10400.237
10410.815



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: CNhs10507

Jaspar motifP-value
MA0002.20.224
MA0003.10.0512
MA0004.10.395
MA0006.10.135
MA0007.10.903
MA0009.10.929
MA0014.10.829
MA0017.11.53374e-4
MA0018.20.05
MA0019.10.568
MA0024.10.0503
MA0025.10.0191
MA0027.10.944
MA0028.10.00764
MA0029.10.7
MA0030.10.176
MA0031.10.161
MA0035.20.183
MA0038.19.33449e-4
MA0039.20.0177
MA0040.10.189
MA0041.10.36
MA0042.10.788
MA0043.10.536
MA0046.14.47539e-9
MA0047.20.707
MA0048.10.203
MA0050.11.53208e-4
MA0051.10.00135
MA0052.10.448
MA0055.10.151
MA0057.10.866
MA0058.10.346
MA0059.10.0159
MA0060.10.99
MA0061.10.765
MA0062.20.00778
MA0065.20.659
MA0066.10.0169
MA0067.10.673
MA0068.10.216
MA0069.10.794
MA0070.10.411
MA0071.10.857
MA0072.10.578
MA0073.10.89
MA0074.10.627
MA0076.10.0765
MA0077.10.393
MA0078.10.0018
MA0079.20.0168
MA0080.20.674
MA0081.10.809
MA0083.17.5881e-6
MA0084.10.665
MA0087.10.989
MA0088.10.881
MA0090.10.688
MA0091.10.0405
MA0092.10.254
MA0093.10.523
MA0099.20.466
MA0100.10.439
MA0101.10.809
MA0102.20.638
MA0103.10.0819
MA0104.20.0603
MA0105.10.0204
MA0106.10.323
MA0107.10.725
MA0108.20.0417
MA0111.10.388
MA0112.20.456
MA0113.10.758
MA0114.10.0033
MA0115.10.00333
MA0116.10.0966
MA0117.10.692
MA0119.10.326
MA0122.10.993
MA0124.10.85
MA0125.10.788
MA0131.10.459
MA0135.10.405
MA0136.10.957
MA0137.20.407
MA0138.20.88
MA0139.10.519
MA0140.10.0441
MA0141.10.849
MA0142.10.434
MA0143.10.356
MA0144.10.573
MA0145.10.0567
MA0146.10.274
MA0147.10.0208
MA0148.10.548
MA0149.10.141
MA0150.10.85
MA0152.10.205
MA0153.11.36444e-6
MA0154.10.802
MA0155.10.705
MA0156.10.568
MA0157.10.00738
MA0159.10.00265
MA0160.10.844
MA0162.10.68
MA0163.10.0834
MA0164.10.215
MA0258.10.979
MA0259.10.062



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: CNhs10507

Novel motifP-value
10.147
100.0897
1000.167
1010.488
1020.785
1030.313
1040.632
1050.661
1060.681
1070.345
1080.725
1090.825
110.224
1100.743
1110.288
1120.577
1130.924
1140.104
1150.556
1160.301
1170.0025
1180.221
1190.923
120.51
1200.0654
1210.0464
1220.381
1230.459
1240.643
1250.15
1260.242
1270.368
1280.67
1290.94
130.833
1300.151
1310.0589
1320.926
1330.493
1340.529
1350.653
1360.105
1370.672
1380.0501
1390.884
140.702
1400.911
1410.144
1420.373
1430.122
1440.365
1450.641
1460.404
1470.435
1480.898
1490.139
150.662
1500.351
1510.604
1520.0253
1530.807
1540.892
1550.511
1560.0906
1570.502
1580.12
1590.15
1600.365
1610.555
1620.701
1630.501
1640.208
1650.863
1660.119
1670.00973
1680.436
1690.0949
170.602
180.0233
190.0952
20.069
200.0786
210.799
220.404
230.896
240.297
250.405
260.966
270.585
280.923
290.121
30.388
300.197
310.496
320.0478
330.537
340.707
350.0374
360.0075
370.855
380.845
390.931
40.492
400.351
410.0875
420.667
430.356
440.397
450.295
460.418
470.856
480.655
490.0374
50.267
500.615
510.842
520.407
530.109
540.571
550.765
560.811
570.177
580.786
590.585
60.77
600.918
610.687
620.289
630.88
640.352
650.795
660.926
670.557
680.17
690.433
70.729
700.429
710.0774
720.62
730.555
740.67
750.0812
763.99234e-4
770.282
780.279
790.72
80.0815
800.371
810.74
820.306
830.16
840.4
850.913
860.917
870.16
880.722
890.934
90.434
900.0139
910.267
920.321
930.171
940.151
950.409
960.143
970.0845
980.416
990.254



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: CNhs10507


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)
0000992 (female gonad)
0000991 (gonad)
0003134 (female reproductive organ)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
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)
0011439 (mouse ovary- 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)

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