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FF:583-22A8

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Name:amnion, adult pregnant day17.5
Species:Mouse (Mus musculus)
Library ID:CNhs10488
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueamnion
dev stage17.5 days pregnant adult
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  SAMD00004853
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10488 CAGE DRX008934 DRR009808
Accession ID Mm9

Library idBAMCTSS
CNhs10488 DRZ001233 DRZ002616
Accession ID Mm10

Library idBAMCTSS
CNhs10488 DRZ012583 DRZ013966
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10488

00
10
100
1000
1000-0.0355
10010.0685
10020.0481
1003-0.138
10040
10050.0879
1006-0.0215
1007-0.0277
10080
10090.0853
101-0.101
10100
1011-0.263
10120
10130.0979
10140.476
1015-0.19
1016-0.138
10170
10180.445
10190
1020
10200
10210
1022-0.315
10230
10240.0846
10250.512
10260.0959
1027-0.048
10280
10290.202
1030.179
10300
10310.0426
1032-0.0877
10330
10340.0959
10350
1036-0.25
10370
10380.102
10390.0409
1040
10400.178
10410



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: CNhs10488

Jaspar motifP-value
MA0002.20.827
MA0003.10.234
MA0004.10.884
MA0006.10.0452
MA0007.10.014
MA0009.10.0918
MA0014.10.301
MA0017.18.48255e-13
MA0018.20.0977
MA0019.10.396
MA0024.12.69002e-7
MA0025.10.929
MA0027.10.169
MA0028.10.413
MA0029.11.87786e-4
MA0030.11.04612e-4
MA0031.18.60996e-7
MA0035.20.0467
MA0038.10.00717
MA0039.21.83139e-4
MA0040.10.188
MA0041.10.426
MA0042.10.553
MA0043.10.552
MA0046.19.87144e-29
MA0047.24.31631e-7
MA0048.10.644
MA0050.10.945
MA0051.10.576
MA0052.10.328
MA0055.10.315
MA0057.10.323
MA0058.10.666
MA0059.10.221
MA0060.19.97623e-12
MA0061.10.232
MA0062.20.683
MA0065.24.73482e-7
MA0066.10.787
MA0067.10.133
MA0068.10.744
MA0069.10.186
MA0070.10.643
MA0071.10.543
MA0072.10.906
MA0073.10.616
MA0074.10.174
MA0076.10.349
MA0077.10.0116
MA0078.10.0653
MA0079.20.00792
MA0080.20.904
MA0081.10.518
MA0083.10.172
MA0084.10.38
MA0087.10.159
MA0088.10.617
MA0090.11.1507e-6
MA0091.10.164
MA0092.10.0714
MA0093.10.905
MA0099.22.42319e-26
MA0100.10.234
MA0101.10.242
MA0102.20.19
MA0103.12.35328e-4
MA0104.20.0524
MA0105.10.923
MA0106.10.227
MA0107.10.132
MA0108.20.492
MA0111.10.664
MA0112.20.00729
MA0113.10.013
MA0114.11.3704e-12
MA0115.11.97441e-10
MA0116.10.754
MA0117.10.117
MA0119.10.629
MA0122.10.624
MA0124.10.227
MA0125.10.334
MA0131.10.983
MA0135.10.597
MA0136.10.932
MA0137.22.90568e-7
MA0138.20.716
MA0139.10.662
MA0140.10.481
MA0141.10.347
MA0142.10.113
MA0143.10.225
MA0144.15.24908e-5
MA0145.10.0126
MA0146.10.021
MA0147.10.0365
MA0148.11.44936e-7
MA0149.10.29
MA0150.10.0115
MA0152.10.85
MA0153.13.75339e-17
MA0154.10.0142
MA0155.10.63
MA0156.10.764
MA0157.19.10388e-5
MA0159.10.0189
MA0160.10.202
MA0162.10.507
MA0163.10.324
MA0164.10.0783
MA0258.10.194
MA0259.10.567



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: CNhs10488

Novel motifP-value
10.826
100.605
1000.305
1010.493
1020.564
1030.196
1040.498
1050.79
1060.0384
1070.0546
1080.785
1090.126
110.334
1100.366
1110.271
1120.0874
1130.595
1140.0725
1150.484
1160.563
1170.185
1180.216
1190.006
120.784
1200.543
1210.38
1220.493
1230.483
1240.184
1250.07
1260.392
1270.682
1280.0156
1290.443
135.37441e-4
1300.0337
1310.504
1320.732
1330.528
1340.806
1350.0846
1360.00273
1370.54
1380.0441
1390.0488
140.467
1400.0875
1410.1
1420.817
1430.776
1440.652
1450.246
1460.258
1470.462
1480.743
1490.0185
150.179
1500.0783
1510.765
1520.0178
1530.641
1540.971
1550.414
1560.0684
1570.587
1580.195
1590.115
1600.345
1610.0809
1620.889
1630.733
1640.0288
1650.505
1660.0288
1670.243
1680.29
1690.0212
170.0198
180.896
190.0135
20.132
200.506
210.221
220.0448
230.0476
240.296
250.598
260.0947
270.709
280.307
290.453
30.18
300.386
310.766
320.0832
330.539
340.763
350.289
360.572
370.0804
380.483
390.754
40.118
400.316
410.516
420.62
430.0702
440.482
450.098
460.51
470.564
480.411
490.123
50.851
500.374
510.687
520.19
530.884
540.333
550.468
560.415
570.394
580.705
590.124
60.856
600.0549
610.26
620.508
630.825
640.921
650.404
660.196
670.544
680.0821
690.148
70.319
700.0163
710.502
720.583
730.0503
740.799
750.26
760.609
770.0448
786.05475e-4
790.532
80.442
800.821
810.339
820.139
830.661
840.443
850.159
860.464
870.15
880.601
890.649
90.704
900.435
910.414
920.0507
930.247
940.14
950.188
960.917
970.382
980.401
990.593



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: CNhs10488


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)
0000305 (amnion)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0004923 (organ component layer)
0005631 (extraembryonic membrane)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000478 (extraembryonic structure)
0010317 (germ layer / neural crest derived structure)
0000158 (membranous layer)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000322 (mouse pregnant day 17.5 sample)
0011386 (mouse amnion - adult pregnant day17.5 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:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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