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FF:437-20E7

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Name:forelimb, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11007
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
dev stage15 days embryo
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  SAMD00005428
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11007 CAGE DRX008967 DRR009841
Accession ID Mm9

Library idBAMCTSS
CNhs11007 DRZ001266 DRZ002649
Accession ID Mm10

Library idBAMCTSS
CNhs11007 DRZ012616 DRZ013999
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

CNhs11007

00
10
100
1000
10000
10010.0196
10020.0533
10030.28
10040
1005-0.0202
1006-0.143
10070.161
10080
10090.135
1010.0966
10100
10110.0924
10120
1013-0.142
10140.621
10150.162
10160.304
10170.107
10180.578
10190
1020
10200
1021-0.0487
1022-0.0704
10230
10240.0525
10250
10260
10270
10280
10290.539
1030.508
10300
10310.388
1032-0.0928
10330.0313
10340
10350
10360.16
10370
10380.0301
1039-0.203
1040
10400.211
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: CNhs11007

Jaspar motifP-value
MA0002.20.00714
MA0003.10.0129
MA0004.10.464
MA0006.10.483
MA0007.10.537
MA0009.10.747
MA0014.10.0754
MA0017.16.91858e-12
MA0018.20.00282
MA0019.10.0827
MA0024.10.00219
MA0025.10.0031
MA0027.10.393
MA0028.10.00838
MA0029.10.913
MA0030.10.0964
MA0031.10.00141
MA0035.23.55888e-8
MA0038.10.856
MA0039.20.00276
MA0040.10.145
MA0041.10.137
MA0042.10.268
MA0043.10.232
MA0046.15.81095e-23
MA0047.26.09246e-4
MA0048.10.0373
MA0050.10.00727
MA0051.15.86207e-5
MA0052.10.509
MA0055.10.882
MA0057.10.647
MA0058.10.261
MA0059.10.877
MA0060.10.913
MA0061.10.288
MA0062.28.13679e-7
MA0065.27.77485e-8
MA0066.10.199
MA0067.10.0352
MA0068.10.868
MA0069.10.941
MA0070.10.406
MA0071.16.44416e-5
MA0072.18.62813e-5
MA0073.10.645
MA0074.10.328
MA0076.10.00776
MA0077.10.934
MA0078.10.17
MA0079.20.309
MA0080.22.74538e-10
MA0081.10.0263
MA0083.10.485
MA0084.10.98
MA0087.10.475
MA0088.10.522
MA0090.10.266
MA0091.10.656
MA0092.10.636
MA0093.10.514
MA0099.20.0175
MA0100.10.361
MA0101.10.0831
MA0102.20.672
MA0103.10.00711
MA0104.20.489
MA0105.10.202
MA0106.10.206
MA0107.10.0779
MA0108.20.79
MA0111.10.4
MA0112.20.00779
MA0113.10.201
MA0114.11.79757e-10
MA0115.14.63698e-4
MA0116.10.1
MA0117.10.0183
MA0119.10.28
MA0122.10.646
MA0124.10.439
MA0125.10.838
MA0131.10.563
MA0135.10.175
MA0136.12.51351e-11
MA0137.20.0576
MA0138.22.79001e-5
MA0139.10.0419
MA0140.18.49481e-5
MA0141.13.45545e-8
MA0142.10.895
MA0143.10.518
MA0144.10.061
MA0145.10.14
MA0146.10.0562
MA0147.10.628
MA0148.10.00624
MA0149.10.00437
MA0150.12.60216e-6
MA0152.10.0175
MA0153.18.67678e-16
MA0154.10.0156
MA0155.10.828
MA0156.11.73348e-7
MA0157.10.2
MA0159.14.67319e-4
MA0160.13.31105e-8
MA0162.10.795
MA0163.10.569
MA0164.10.757
MA0258.10.0011
MA0259.10.828



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: CNhs11007

Novel motifP-value
10.187
100.849
1000.625
1010.851
1020.397
1030.183
1040.379
1050.74
1060.126
1070.772
1080.713
1090.0311
110.0847
1100.559
1110.0464
1120.0921
1130.696
1140.0137
1150.935
1160.639
1170.423
1180.321
1190.131
120.516
1200.448
1210.114
1220.995
1230.216
1240.246
1250.661
1260.267
1270.273
1280.375
1290.441
130.984
1300.155
1310.434
1320.415
1330.0707
1340.835
1350.831
1360.0572
1370.86
1380.423
1390.0405
140.349
1400.644
1410.737
1420.303
1430.55
1440.282
1450.517
1460.217
1470.256
1480.361
1490.333
150.0265
1500.899
1510.0101
1520.104
1530.581
1540.415
1550.814
1560.479
1570.763
1580.466
1590.305
1600.243
1610.434
1620.891
1630.121
1640.383
1650.0715
1660.16
1670.701
1680.694
1690.14
170.24
180.346
190.567
20.891
200.777
210.733
220.413
230.809
240.397
250.145
260.35
270.323
280.213
290.297
30.351
300.979
310.359
320.445
330.392
340.548
350.16
360.0983
370.103
380.246
390.649
40.769
400.0293
410.151
420.902
430.278
440.00959
450.245
460.774
470.159
480.0898
490.247
50.503
500.696
510.637
520.694
530.883
540.503
550.316
560.57
570.744
580.435
590.108
60.781
600.273
610.596
620.167
630.267
640.399
650.172
660.385
670.457
680.0345
690.602
70.51
700.0269
710.832
720.165
730.0382
740.903
750.0715
760.91
770.361
780.598
790.879
80.107
800.00389
810.376
820.166
830.556
840.38
850.0378
860.884
877.79746e-6
880.983
890.195
90.966
900.468
910.683
920.92
930.628
940.262
950.00882
960.698
970.839
980.295
990.547



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: CNhs11007


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)
0000922 (embryo)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011351 (mouse forelimb- embryo E15 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:0006603 (presumptive mesoderm)
UBERON:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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