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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;89
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;89
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;89
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;89
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.ctss.bed.gz

Revision as of 18:59, 4 August 2017


Name:vagina, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10502
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuevagina
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  SAMD00005786
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10502 CAGE DRX009130 DRR010004
Accession ID Mm9

Library idBAMCTSS
CNhs10502 DRZ001429 DRZ002812
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

CNhs10502

00
10
100
1000
10000.0422
10010.141
1002-0.0422
10030.148
10040.216
10050.0455
1006-0.0101
1007-0.0195
10080
10090.169
1010.0595
10100
1011-0.0459
10120
10130.0984
1014-0.0874
1015-0.147
1016-0.0393
10170.553
10180.94
10190
1020
10200
10210
10220.014
10230
10240.0761
10250.0549
10260
1027-0.00502
10280.0844
10290.14
1030.197
10300
10310.136
10320.0853
10330.00913
10340.0844
10350
10360.053
10370
1038-0.0466
1039-0.159
1040
10400.137
10410.0844



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: CNhs10502

Jaspar motifP-value
MA0002.20.0942
MA0003.10.428
MA0004.10.911
MA0006.10.0367
MA0007.10.941
MA0009.10.184
MA0014.10.511
MA0017.13.86391e-4
MA0018.20.277
MA0019.10.167
MA0024.15.23007e-4
MA0025.10.467
MA0027.10.351
MA0028.10.0517
MA0029.10.212
MA0030.10.558
MA0031.10.348
MA0035.24.4504e-6
MA0038.10.289
MA0039.29.5958e-4
MA0040.10.877
MA0041.10.0273
MA0042.10.031
MA0043.10.262
MA0046.17.44021e-7
MA0047.20.476
MA0048.10.994
MA0050.10.0526
MA0051.10.536
MA0052.10.545
MA0055.10.384
MA0057.10.0655
MA0058.10.579
MA0059.10.398
MA0060.16.37041e-8
MA0061.10.533
MA0062.20.043
MA0065.20.719
MA0066.10.929
MA0067.10.288
MA0068.10.566
MA0069.10.561
MA0070.10.612
MA0071.10.0885
MA0072.10.583
MA0073.10.922
MA0074.10.514
MA0076.10.0191
MA0077.10.21
MA0078.10.347
MA0079.20.0188
MA0080.20.0131
MA0081.10.359
MA0083.10.0321
MA0084.10.584
MA0087.10.744
MA0088.10.808
MA0090.10.121
MA0091.10.351
MA0092.10.279
MA0093.10.794
MA0099.21.34429e-32
MA0100.10.0932
MA0101.10.389
MA0102.20.132
MA0103.11.61034e-4
MA0104.20.0807
MA0105.10.705
MA0106.10.00533
MA0107.10.103
MA0108.21.0896e-9
MA0111.10.378
MA0112.20.0629
MA0113.10.382
MA0114.10.00126
MA0115.14.52519e-4
MA0116.10.672
MA0117.10.668
MA0119.10.644
MA0122.10.577
MA0124.10.366
MA0125.10.279
MA0131.10.278
MA0135.10.686
MA0136.10.042
MA0137.20.0982
MA0138.20.846
MA0139.10.78
MA0140.16.89958e-5
MA0141.10.00218
MA0142.10.348
MA0143.10.035
MA0144.10.0157
MA0145.10.00383
MA0146.10.441
MA0147.10.0734
MA0148.10.951
MA0149.10.268
MA0150.10.0132
MA0152.10.839
MA0153.12.29093e-7
MA0154.10.169
MA0155.10.679
MA0156.10.203
MA0157.10.0735
MA0159.10.983
MA0160.10.028
MA0162.10.849
MA0163.10.827
MA0164.10.776
MA0258.10.277
MA0259.10.145



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: CNhs10502

Novel motifP-value
10.778
100.667
1000.364
1010.778
1020.263
1030.408
1040.235
1050.23
1066.44931e-4
1070.0115
1080.762
1090.291
110.955
1100.557
1110.502
1120.506
1130.83
1140.817
1150.185
1160.335
1170.458
1180.128
1190.0135
120.514
1200.838
1210.267
1220.237
1230.568
1240.712
1250.553
1260.268
1270.585
1280.00317
1290.595
130.0461
1300.496
1310.26
1320.722
1330.275
1340.831
1350.555
1360.123
1370.14
1380.0163
1390.198
140.412
1400.0484
1410.483
1420.839
1430.804
1440.659
1450.247
1460.157
1470.186
1480.492
1490.272
150.703
1500.349
1510.403
1520.00378
1530.154
1540.643
1550.879
1560.887
1570.187
1580.409
1590.239
1600.37
1610.829
1620.783
1630.396
1640.763
1650.308
1660.493
1670.192
1680.944
1690.0432
170.0131
180.893
190.0655
20.164
200.531
210.00895
220.399
230.0723
240.0538
250.182
260.0405
270.987
280.543
290.924
30.641
300.061
310.965
320.846
330.922
340.937
350.167
360.179
370.159
380.786
390.375
40.79
400.374
410.348
420.437
430.262
440.316
450.12
460.22
470.868
480.937
490.372
50.827
500.518
510.59
520.101
530.174
540.376
550.82
560.553
570.702
580.481
590.196
60.18
600.126
610.258
620.786
630.298
640.582
650.676
660.575
670.698
680.373
690.893
70.769
700.0709
710.386
720.609
730.0122
740.83
750.566
760.108
770.0171
780.0632
790.833
80.717
800.0814
810.153
820.549
830.211
840.446
850.109
860.287
870.187
880.82
890.893
90.153
900.609
910.784
920.262
930.249
940.931
950.643
960.499
970.25
980.99
990.223



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: CNhs10502


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)
0000996 (vagina)
0003134 (female reproductive organ)
0000479 (tissue)
0005156 (reproductive structure)
0004119 (endoderm-derived structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/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)
0011438 (mouse vagina- 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:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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