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FF:1395-42I2

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Name:cerebellum, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11135
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecerebellum
dev stage30 days 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  SAMD00005275
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11135 CAGE DRX008942 DRR009816
Accession ID Mm9

Library idBAMCTSS
CNhs11135 DRZ001241 DRZ002624
Accession ID Mm10

Library idBAMCTSS
CNhs11135 DRZ012591 DRZ013974
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

CNhs11135

00
10.635
100
1000
10000.00582
10010.0688
1002-0.104
10030.341
10040
10050.0125
10060.767
10070.122
10080
1009-0.0572
101-0.112
10100
10110.341
10120.353
10130.167
1014-0.0874
1015-0.0754
1016-0.0483
10170
10180
10190
1020
10200
10210
1022-0.0704
10230
10240.0341
10250
10260
10270.392
10280
10290.343
103-0.0665
10300
1031-0.299
10320.286
1033-0.0526
10340
10350
1036-0.183
10370
10380.221
10390.0424
1040
1040-0.231
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: CNhs11135

Jaspar motifP-value
MA0002.27.78821e-4
MA0003.10.208
MA0004.10.301
MA0006.10.14
MA0007.10.434
MA0009.10.325
MA0014.10.393
MA0017.14.14582e-6
MA0018.20.0276
MA0019.10.471
MA0024.10.0825
MA0025.10.00829
MA0027.10.0273
MA0028.10.034
MA0029.10.623
MA0030.10.511
MA0031.10.402
MA0035.20.0156
MA0038.10.565
MA0039.20.00572
MA0040.10.34
MA0041.10.919
MA0042.10.198
MA0043.10.278
MA0046.13.04348e-12
MA0047.26.35817e-4
MA0048.10.116
MA0050.18.31028e-5
MA0051.16.48027e-4
MA0052.10.394
MA0055.10.0719
MA0057.10.263
MA0058.10.273
MA0059.10.13
MA0060.10.329
MA0061.10.0109
MA0062.26.8731e-5
MA0065.21.98177e-6
MA0066.10.397
MA0067.10.483
MA0068.10.625
MA0069.10.094
MA0070.10.78
MA0071.10.943
MA0072.10.163
MA0073.10.871
MA0074.10.152
MA0076.10.101
MA0077.10.48
MA0078.10.948
MA0079.20.508
MA0080.22.34951e-10
MA0081.10.109
MA0083.10.00116
MA0084.10.988
MA0087.10.365
MA0088.10.127
MA0090.10.042
MA0091.10.479
MA0092.10.366
MA0093.10.329
MA0099.27.10762e-5
MA0100.10.174
MA0101.10.00953
MA0102.20.0908
MA0103.10.477
MA0104.20.72
MA0105.10.00252
MA0106.10.0517
MA0107.10.0151
MA0108.22.99667e-9
MA0111.10.951
MA0112.20.00619
MA0113.10.689
MA0114.11.10498e-6
MA0115.10.00194
MA0116.10.0485
MA0117.10.86
MA0119.10.202
MA0122.10.861
MA0124.10.8
MA0125.10.15
MA0131.10.714
MA0135.10.943
MA0136.18.29967e-16
MA0137.20.244
MA0138.21.43887e-4
MA0139.10.336
MA0140.14.05244e-5
MA0141.10.0252
MA0142.10.971
MA0143.10.914
MA0144.10.103
MA0145.10.119
MA0146.10.044
MA0147.10.587
MA0148.10.00173
MA0149.10.131
MA0150.10.0672
MA0152.10.733
MA0153.11.16364e-14
MA0154.10.0539
MA0155.10.431
MA0156.12.40455e-12
MA0157.10.192
MA0159.10.0164
MA0160.10.00926
MA0162.10.221
MA0163.10.00206
MA0164.10.676
MA0258.10.118
MA0259.10.782



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: CNhs11135

Novel motifP-value
10.422
100.0725
1000.582
1010.633
1020.776
1030.0247
1040.779
1050.273
1060.0464
1070.17
1080.507
1090.0065
110.212
1100.0879
1110.22
1120.0138
1130.511
1140.914
1150.463
1160.184
1170.00738
1180.409
1190.223
120.81
1200.822
1210.368
1220.855
1230.0247
1240.325
1250.354
1260.0466
1270.13
1280.0397
1290.197
137.14032e-8
1300.0577
1310.526
1320.861
1330.173
1340.408
1350.94
1360.139
1370.328
1380.798
1390.295
140.864
1400.313
1410.797
1420.898
1430.515
1440.6
1459.24022e-5
1460.429
1470.121
1480.836
1490.8
150.211
1500.0557
1510.98
1520.0613
1530.684
1540.804
1550.43
1560.0669
1570.302
1580.285
1590.491
1600.297
1610.681
1620.839
1630.992
1640.0277
1650.0723
1660.106
1670.84
1680.22
1690.008
170.107
180.928
190.192
20.815
200.0433
210.163
220.193
230.597
240.0665
250.289
261.89405e-7
270.341
280.91
290.0153
30.0572
300.938
310.84
320.881
330.175
340.752
350.378
360.183
370.0322
380.455
390.466
40.384
400.0489
410.266
420.216
430.162
440.257
450.668
460.0962
470.365
480.301
490.312
50.252
500.308
510.668
520.226
530.734
540.958
550.858
560.506
570.679
580.143
590.113
60.722
600.0249
610.126
620.0869
630.237
640.966
650.361
660.598
670.732
680.677
690.554
70.00309
700.236
710.00184
720.31
730.0355
740.862
750.0611
760.543
770.284
788.32099e-4
790.892
80.0642
800.917
810.862
820.469
830.3
840.424
850.428
860.225
870.178
880.788
890.431
90.49
900.231
910.346
920.212
930.063
940.827
950.0126
960.573
970.836
980.341
990.637



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: CNhs11135


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)
0000955 (brain)
0002037 (cerebellum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011250 (mouse cerebellum- neonate N30 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:0006215 (rhombic lip)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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