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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005396
|DRA_sample_Accession=CAGE@SAMD00005396
|accession_numbers=CAGE;DRX009075;DRR009949;DRZ001374;DRZ002757
|accession_numbers=CAGE;DRX009075;DRR009949;DRZ001374;DRZ002757;DRZ012724;DRZ014107
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001987,UBERON:0000479,UBERON:0005156,UBERON:0004119,UBERON:0000062,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000478,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001987,UBERON:0000479,UBERON:0005156,UBERON:0004119,UBERON:0000062,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000478,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:39, 10 August 2017


Name:placenta, adult pregnant day17
Species:Mouse (Mus musculus)
Library ID:CNhs10464
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueplacenta
dev stage17 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  SAMD00005396
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10464 CAGE DRX009075 DRR009949
Accession ID Mm9

Library idBAMCTSS
CNhs10464 DRZ001374 DRZ002757
Accession ID Mm10

Library idBAMCTSS
CNhs10464 DRZ012724 DRZ014107
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

CNhs10464

00
10
100
1000
1000-0.0355
10010.00614
1002-0.0327
1003-0.156
10040
10050
1006-9.149961e-4
10070.0104
10080
10090.156
101-0.0736
10100
1011-0.0489
10120
10130.135
10140.308
1015-0.195
1016-0.152
10170
10180.562
10190
1020
10200
10210
1022-0.162
10230
10240.0741
10250.356
10260
1027-0.048
10280.0834
10290.168
1030
10300
1031-0.0143
10320.0829
1033-0.0665
10340
10350
1036-0.266
10370
10380.162
1039-0.149
1040
10400.143
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: CNhs10464

Jaspar motifP-value
MA0002.20.707
MA0003.10.169
MA0004.10.786
MA0006.10.118
MA0007.10.625
MA0009.10.0217
MA0014.10.119
MA0017.10.0189
MA0018.20.285
MA0019.10.135
MA0024.13.609e-4
MA0025.10.325
MA0027.10.655
MA0028.10.0684
MA0029.10.00252
MA0030.10.0215
MA0031.12.82025e-5
MA0035.20.0159
MA0038.10.623
MA0039.29.16484e-5
MA0040.10.469
MA0041.10.21
MA0042.10.726
MA0043.10.682
MA0046.10.453
MA0047.20.144
MA0048.10.442
MA0050.10.298
MA0051.10.0466
MA0052.10.0504
MA0055.10.0104
MA0057.10.282
MA0058.10.324
MA0059.10.268
MA0060.17.30053e-4
MA0061.10.941
MA0062.20.0109
MA0065.20.00531
MA0066.10.297
MA0067.10.0623
MA0068.10.876
MA0069.10.93
MA0070.10.619
MA0071.10.161
MA0072.10.731
MA0073.10.884
MA0074.10.905
MA0076.10.132
MA0077.10.136
MA0078.10.311
MA0079.20.00219
MA0080.20.968
MA0081.10.879
MA0083.10.0104
MA0084.10.62
MA0087.10.889
MA0088.10.416
MA0090.13.76677e-4
MA0091.10.0329
MA0092.10.933
MA0093.10.664
MA0099.21.44241e-23
MA0100.10.317
MA0101.10.574
MA0102.20.808
MA0103.10.0822
MA0104.20.14
MA0105.10.051
MA0106.10.383
MA0107.10.556
MA0108.20.00406
MA0111.10.535
MA0112.20.14
MA0113.10.637
MA0114.10.00245
MA0115.16.31628e-4
MA0116.10.351
MA0117.10.0272
MA0119.10.00947
MA0122.10.424
MA0124.10.154
MA0125.10.95
MA0131.10.773
MA0135.10.74
MA0136.10.559
MA0137.20.00157
MA0138.20.388
MA0139.10.993
MA0140.10.673
MA0141.10.478
MA0142.10.137
MA0143.10.326
MA0144.10.0111
MA0145.10.0718
MA0146.10.0105
MA0147.10.101
MA0148.10.707
MA0149.10.554
MA0150.10.00145
MA0152.10.207
MA0153.10.891
MA0154.10.186
MA0155.10.704
MA0156.10.243
MA0157.10.00329
MA0159.10.1
MA0160.10.182
MA0162.10.981
MA0163.10.454
MA0164.10.0322
MA0258.10.352
MA0259.10.492



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: CNhs10464

Novel motifP-value
10.496
100.779
1000.678
1010.803
1020.174
1030.809
1040.77
1050.935
1060.426
1070.294
1080.972
1090.672
110.84
1100.682
1110.365
1120.144
1130.565
1140.758
1150.839
1160.362
1170.174
1180.919
1190.29
120.585
1200.149
1210.264
1220.74
1230.0315
1240.242
1250.226
1260.665
1270.915
1280.432
1290.931
130.0147
1300.0471
1310.751
1320.755
1330.873
1340.539
1350.0795
1369.28448e-4
1370.416
1380.017
1390.153
140.943
1400.132
1410.864
1420.63
1430.979
1440.626
1450.889
1460.614
1470.286
1480.507
1490.878
150.8
1500.103
1510.321
1520.0113
1530.692
1540.491
1550.258
1560.00505
1570.359
1580.0596
1590.825
1600.464
1610.00682
1620.737
1630.207
1640.141
1650.907
1660.0171
1670.0888
1680.215
1690.079
170.108
180.969
190.0198
20.512
200.263
211
220.0365
230.0828
240.25
250.899
260.566
270.195
280.552
290.57
30.829
300.538
310.332
320.592
330.774
340.913
350.00474
360.15
370.0986
380.618
390.517
40.0417
400.637
410.609
420.812
430.948
440.841
450.124
460.619
470.506
480.612
490.63
50.629
500.245
510.905
520.453
530.72
540.633
550.291
560.942
570.191
580.609
590.775
60.996
600.233
610.299
620.546
630.455
640.372
650.698
660.829
670.469
680.188
690.223
70.569
700.119
710.253
720.574
730.00626
740.776
750.475
760.349
770.699
780.00868
790.291
80.0628
800.517
810.319
820.917
830.615
840.547
850.673
860.59
870.00236
880.326
890.825
90.719
900.0909
910.615
920.383
930.132
940.0126
950.203
960.878
970.499
980.383
990.213



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: CNhs10464


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)
0000321 (mouse pregnant day 17 sample)
0011384 (mouse placenta- adult pregnant day17 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)

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