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FF:1532-43E7

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Name:eyeball, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs11140
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage1 day neonate
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  SAMD00004944
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11140 CAGE DRX008960 DRR009834
Accession ID Mm9

Library idBAMCTSS
CNhs11140 DRZ001259 DRZ002642
Accession ID Mm10

Library idBAMCTSS
CNhs11140 DRZ012609 DRZ013992
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

CNhs11140

00
10.18
100
1000.18
10000.0262
10010.173
10020.297
10030.106
10040.139
10050
10060.192
10070.119
10080
1009-0.00487
1010.0638
10100
10110.0471
10120.141
1013-0.0989
10140.248
10150.138
10160.198
10170
10180
10190
1020
10200
10210
10220.0991
10230
1024-0.0899
1025-0.0581
10260
10270.899
10280
10290.442
1030.449
10300.0524
10310.323
10320.0287
10330.0524
10340
10350.0524
10360.054
10370
10380.0273
1039-0.123
1040
1040-6.461034e-4
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: CNhs11140

Jaspar motifP-value
MA0002.21.43848e-4
MA0003.10.178
MA0004.10.285
MA0006.10.229
MA0007.10.222
MA0009.10.124
MA0014.10.172
MA0017.13.76448e-8
MA0018.20.466
MA0019.10.333
MA0024.10.00483
MA0025.10.0249
MA0027.10.614
MA0028.10.152
MA0029.10.284
MA0030.10.603
MA0031.10.129
MA0035.24.02174e-4
MA0038.10.00356
MA0039.20.00335
MA0040.10.0647
MA0041.10.34
MA0042.10.927
MA0043.10.493
MA0046.11.49811e-23
MA0047.25.91798e-5
MA0048.10.516
MA0050.17.55452e-4
MA0051.10.00405
MA0052.10.931
MA0055.10.528
MA0057.10.123
MA0058.10.245
MA0059.10.338
MA0060.15.85624e-7
MA0061.10.0238
MA0062.23.58204e-4
MA0065.24.55166e-8
MA0066.10.353
MA0067.10.874
MA0068.10.455
MA0069.10.0282
MA0070.10.693
MA0071.10.876
MA0072.10.0583
MA0073.10.519
MA0074.10.267
MA0076.10.406
MA0077.10.0207
MA0078.10.876
MA0079.20.586
MA0080.24.10711e-13
MA0081.10.0229
MA0083.10.474
MA0084.10.102
MA0087.10.463
MA0088.10.0926
MA0090.10.531
MA0091.10.0343
MA0092.10.554
MA0093.10.306
MA0099.27.48342e-7
MA0100.10.689
MA0101.10.0193
MA0102.20.206
MA0103.18.70155e-4
MA0104.20.963
MA0105.10.019
MA0106.10.375
MA0107.10.0266
MA0108.20.0921
MA0111.10.904
MA0112.20.00144
MA0113.10.122
MA0114.11.08843e-7
MA0115.17.84165e-6
MA0116.10.0346
MA0117.10.75
MA0119.10.0816
MA0122.10.884
MA0124.10.41
MA0125.10.00434
MA0131.10.611
MA0135.10.487
MA0136.11.02566e-16
MA0137.20.00243
MA0138.20.553
MA0139.10.0986
MA0140.13.61328e-4
MA0141.11.78851e-4
MA0142.10.237
MA0143.10.0289
MA0144.10.00387
MA0145.10.0343
MA0146.10.0285
MA0147.10.714
MA0148.18.38187e-4
MA0149.10.0336
MA0150.10.0269
MA0152.10.275
MA0153.15.46415e-25
MA0154.10.00643
MA0155.10.801
MA0156.12.24701e-9
MA0157.10.0672
MA0159.10.00819
MA0160.16.92746e-4
MA0162.10.42
MA0163.19.0095e-4
MA0164.10.83
MA0258.10.0176
MA0259.10.979



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: CNhs11140

Novel motifP-value
10.189
100.164
1000.595
1010.903
1020.592
1030.0292
1040.662
1050.423
1060.0408
1070.231
1080.913
1090.00608
110.0365
1100.103
1110.00406
1120.00671
1130.996
1140.0361
1150.911
1160.0964
1170.0228
1180.317
1190.0826
120.313
1200.509
1210.247
1220.982
1230.473
1240.974
1250.127
1260.159
1270.0592
1280.156
1290.613
130.00234
1300.877
1310.275
1320.673
1330.883
1340.646
1350.553
1360.0122
1370.532
1380.263
1390.0789
140.902
1400.368
1410.0748
1420.786
1430.191
1440.664
1450.0659
1460.292
1470.75
1480.425
1490.216
150.0734
1500.217
1510.403
1520.0201
1530.88
1540.715
1550.278
1560.795
1570.812
1580.338
1590.711
1600.48
1610.311
1620.863
1630.591
1640.00512
1650.0541
1660.437
1670.822
1680.881
1690.00682
170.0478
180.589
190.321
20.456
200.466
210.192
220.2
230.457
240.0431
250.513
260.0234
270.409
280.282
290.0454
30.0862
300.607
310.531
320.437
330.208
340.616
350.773
360.355
370.0138
380.27
390.382
40.599
400.232
410.269
420.331
430.208
440.0904
450.35
460.198
470.0757
480.0646
490.242
50.181
500.701
510.532
520.247
530.981
540.623
550.566
560.332
570.834
580.279
590.0152
60.694
600.0265
610.347
620.142
630.0795
640.476
650.147
660.901
670.701
680.0625
690.996
70.1
700.00956
710.0293
720.165
730.00756
740.45
750.0372
760.59
770.116
780.0323
790.183
80.0607
800.275
810.395
820.0268
830.614
840.21
850.0907
860.139
870.00543
880.495
890.0646
90.611
900.241
910.949
920.0841
930.524
940.482
950.0108
960.791
970.961
980.361
990.558



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: CNhs11140


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)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011252 (mouse eyeball- neonate N01 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:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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