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FF:539-13I7

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Name:placenta, adult pregnant day10
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueplacenta
dev stage10 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  DRS008937
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs10472

00
10
100
1000
1000-0.0258
10010.0641
10020.0147
1003-0.175
10040.129
10050.094
1006-0.0595
10070.00944
10080
10090.0343
1010.092
10100
1011-0.016
10120
10130.177
10140.00644
1015-0.115
1016-0.234
10170
10180.316
10190
1020
10200
10210
1022-0.124
10230
10240.0916
10250.0916
10260
1027-0.048
10280
10290.105
1030
10300
10310.0645
1032-0.213
1033-0.0665
10340
10350
1036-0.0518
10370
1038-0.127
1039-0.0886
1040
10400.0719
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: CNhs10472

Jaspar motifP-value
MA0002.20.0682
MA0003.10.08
MA0004.10.411
MA0006.10.0393
MA0007.10.817
MA0009.10.5
MA0014.10.358
MA0017.10.0312
MA0018.20.924
MA0019.10.321
MA0024.10.53
MA0025.10.354
MA0027.10.00607
MA0028.10.352
MA0029.18.2156e-6
MA0030.10.332
MA0031.10.0545
MA0035.20.0476
MA0038.10.413
MA0039.26.56889e-5
MA0040.10.779
MA0041.10.45
MA0042.10.732
MA0043.10.425
MA0046.10.689
MA0047.20.593
MA0048.10.2
MA0050.10.021
MA0051.10.132
MA0052.10.00158
MA0055.10.0294
MA0057.10.152
MA0058.10.16
MA0059.10.923
MA0060.10.171
MA0061.10.233
MA0062.20.0147
MA0065.20.0543
MA0066.10.78
MA0067.10.632
MA0068.10.328
MA0069.10.509
MA0070.10.385
MA0071.10.922
MA0072.10.731
MA0073.10.378
MA0074.10.469
MA0076.10.531
MA0077.10.0728
MA0078.10.235
MA0079.20.00481
MA0080.23.74983e-4
MA0081.10.596
MA0083.10.538
MA0084.10.126
MA0087.10.61
MA0088.10.19
MA0090.10.0482
MA0091.10.0874
MA0092.10.626
MA0093.10.383
MA0099.23.74413e-30
MA0100.10.317
MA0101.10.052
MA0102.20.631
MA0103.10.881
MA0104.20.551
MA0105.10.687
MA0106.10.0756
MA0107.10.0678
MA0108.25.07198e-5
MA0111.10.263
MA0112.20.0137
MA0113.10.854
MA0114.10.0202
MA0115.10.0282
MA0116.10.92
MA0117.10.468
MA0119.10.0618
MA0122.10.611
MA0124.10.137
MA0125.10.869
MA0131.10.933
MA0135.10.6
MA0136.10.00117
MA0137.20.0457
MA0138.20.0795
MA0139.10.802
MA0140.10.926
MA0141.10.678
MA0142.10.0535
MA0143.10.111
MA0144.10.00277
MA0145.10.0334
MA0146.10.0674
MA0147.10.638
MA0148.10.0791
MA0149.10.111
MA0150.17.12013e-4
MA0152.10.66
MA0153.10.297
MA0154.10.0696
MA0155.10.897
MA0156.11.95255e-4
MA0157.10.245
MA0159.10.0517
MA0160.10.335
MA0162.10.701
MA0163.10.955
MA0164.10.0254
MA0258.10.182
MA0259.10.742



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: CNhs10472

Novel motifP-value
10.603
100.693
1000.718
1010.134
1020.133
1030.552
1040.732
1050.405
1060.0529
1070.0653
1080.405
1090.421
110.896
1100.521
1110.399
1120.00618
1130.948
1140.382
1150.823
1160.739
1170.0766
1180.756
1190.101
120.877
1200.964
1210.192
1220.631
1230.0141
1240.0457
1250.502
1260.483
1270.801
1280.283
1290.826
130.0028
1300.0439
1310.921
1320.704
1330.437
1340.283
1350.147
1360.0159
1370.0961
1380.326
1390.184
140.787
1400.674
1410.394
1420.455
1430.235
1440.45
1450.821
1460.834
1470.0376
1480.319
1490.802
150.25
1500.0885
1510.957
1520.00983
1530.473
1540.646
1550.622
1560.111
1570.151
1580.00768
1590.498
1600.495
1610.154
1620.788
1630.0323
1640.0201
1650.838
1660.735
1670.0649
1680.279
1690.0444
170.119
180.697
190.0222
20.183
200.277
210.489
220.035
230.407
240.103
250.848
260.594
270.44
280.504
290.053
30.78
300.334
310.309
320.686
330.629
340.729
350.0281
360.473
370.0381
380.791
390.978
40.188
400.83
410.997
420.801
430.572
440.709
450.044
460.718
470.677
480.81
490.545
50.92
500.101
510.949
520.259
530.891
540.793
550.515
560.971
570.338
580.645
590.284
60.461
600.289
610.209
620.512
630.794
640.499
650.765
660.722
670.626
680.525
690.213
70.487
700.186
710.787
720.298
730.0054
740.837
750.281
760.887
770.392
780.00392
790.177
80.326
800.69
810.585
820.971
830.356
840.664
850.524
860.594
870.0803
880.537
890.619
90.61
900.198
910.195
920.713
930.619
940.0258
950.225
960.979
970.72
980.69
990.493



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: CNhs10472


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)
0001987 (placenta)
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)
0000478 (extraembryonic structure)
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)
0000317 (mouse pregnant tissue sample)
0000320 (mouse pregnant day 10 sample)
0011381 (mouse placenta- adult pregnant day10 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:0005795 (embryonic uterus)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0003124 (chorion)
UBERON:0010316 (germ layer / neural crest)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
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