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FF:508-5B2

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Name:liver, adult pregnant day01
Species:Mouse (Mus musculus)
Library ID:CNhs10466
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage1 day pregnant adult
sexmixture
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  SAMD00005992
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10466 CAGE DRX009014 DRR009888
Accession ID Mm9

Library idBAMCTSS
CNhs10466 DRZ001313 DRZ002696
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

CNhs10466

00
10
100
1000
10000.0773
10010.03
1002-0.116
10030.112
10040
10050
1006-0.143
1007-0.228
10080
10090.00269
1010.0309
10100
1011-0.224
10120
10130.466
1014-0.0874
1015-0.382
1016-0.318
10170
10180
10190
1020
10200
10210
10220.736
10230
10240
10250.437
10260
1027-0.048
10280
1029-0.0989
103-0.0848
10300
1031-0.417
1032-0.397
10330.0463
10340.816
10350
1036-0.183
10370
1038-0.14
10390.803
1040
1040-0.19
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: CNhs10466

Jaspar motifP-value
MA0002.20.216
MA0003.10.4
MA0004.10.427
MA0006.10.273
MA0007.10.0722
MA0009.10.983
MA0014.10.114
MA0017.14.99121e-23
MA0018.22.1753e-4
MA0019.10.596
MA0024.13.16662e-4
MA0025.10.0011
MA0027.10.883
MA0028.10.318
MA0029.10.235
MA0030.10.00618
MA0031.10.00221
MA0035.20.0457
MA0038.10.465
MA0039.20.26
MA0040.10.291
MA0041.10.864
MA0042.10.945
MA0043.10.315
MA0046.11.74228e-96
MA0047.23.20453e-7
MA0048.10.261
MA0050.10.00108
MA0051.19.61359e-4
MA0052.10.0109
MA0055.10.226
MA0057.10.459
MA0058.10.298
MA0059.10.0546
MA0060.12.36029e-5
MA0061.10.611
MA0062.20.44
MA0065.23.90538e-15
MA0066.10.0629
MA0067.10.155
MA0068.10.462
MA0069.10.307
MA0070.10.462
MA0071.19.60444e-5
MA0072.11.49741e-4
MA0073.10.832
MA0074.10.226
MA0076.10.716
MA0077.10.0602
MA0078.10.847
MA0079.20.375
MA0080.20.894
MA0081.10.857
MA0083.10.00162
MA0084.10.488
MA0087.10.376
MA0088.10.205
MA0090.10.707
MA0091.10.798
MA0092.10.118
MA0093.10.446
MA0099.20.63
MA0100.10.314
MA0101.10.96
MA0102.20.304
MA0103.10.115
MA0104.20.548
MA0105.10.203
MA0106.10.125
MA0107.10.703
MA0108.20.00302
MA0111.10.606
MA0112.26.71493e-6
MA0113.10.315
MA0114.14.44663e-22
MA0115.14.69992e-10
MA0116.10.153
MA0117.10.644
MA0119.10.0192
MA0122.10.586
MA0124.10.578
MA0125.10.369
MA0131.10.898
MA0135.10.772
MA0136.10.873
MA0137.20.00754
MA0138.20.361
MA0139.10.208
MA0140.10.686
MA0141.13.72461e-6
MA0142.10.242
MA0143.10.296
MA0144.10.112
MA0145.10.0383
MA0146.10.103
MA0147.10.437
MA0148.11.36926e-10
MA0149.10.00917
MA0150.10.00614
MA0152.10.984
MA0153.14.37719e-65
MA0154.10.144
MA0155.10.941
MA0156.10.923
MA0157.10.00151
MA0159.13.47374e-4
MA0160.19.14822e-5
MA0162.10.433
MA0163.10.0116
MA0164.10.774
MA0258.10.00145
MA0259.10.836



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: CNhs10466

Novel motifP-value
10.0869
100.213
1000.498
1010.642
1020.216
1030.0127
1040.807
1050.646
1060.0966
1070.156
1080.741
1090.0295
110.0472
1100.0732
1110.0338
1120.0155
1130.996
1140.00434
1150.365
1160.843
1170.0722
1180.435
1190.0606
120.478
1200.696
1210.517
1220.358
1230.418
1240.484
1250.339
1260.261
1270.774
1280.0349
1290.652
139.49059e-5
1300.74
1310.475
1320.498
1330.743
1340.718
1350.369
1360.441
1370.802
1380.499
1390.341
140.461
1400.0487
1410.532
1420.265
1430.869
1440.491
1450.0639
1460.42
1470.408
1480.661
1490.0909
150.138
1500.218
1510.445
1520.0648
1530.423
1540.958
1550.439
1560.101
1570.745
1580.567
1590.375
1600.336
1610.88
1620.615
1630.211
1640.0336
1650.566
1660.276
1670.264
1680.952
1690.00228
170.0635
180.871
190.0473
20.736
200.522
210.573
220.123
230.256
240.148
250.554
260.00637
270.698
280.462
290.197
30.0638
300.777
310.405
320.178
330.313
340.854
350.46
360.0718
370.0652
380.254
390.317
40.934
400.103
410.933
420.358
430.0808
440.0591
450.652
460.155
470.328
480.102
490.0417
50.184
500.666
510.308
520.452
530.671
540.331
550.659
560.457
570.902
580.243
590.316
60.786
600.146
610.169
620.0729
630.0842
640.432
650.158
660.514
670.93
680.184
690.899
70.194
700.0152
710.0443
720.65
730.0484
740.591
750.0173
760.871
770.416
780.0295
790.947
80.00709
800.543
810.559
820.0201
830.306
840.274
850.0449
860.0893
870.135
880.826
890.0544
90.774
900.149
910.652
920.25
930.115
940.822
950.205
960.308
970.232
980.334
990.0826



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: CNhs10466


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary 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)
0000318 (mouse pregnant day 1 sample)
0011379 (mouse liver- adult pregnant day01 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)

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