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FF:10235-104A1

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13031
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 15
sexmale
ageP15
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004956
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13031 CAGE DRX009132 DRR010006
Accession ID Mm9

Library idBAMCTSS
CNhs13031 DRZ001431 DRZ002814
Accession ID Mm10

Library idBAMCTSS
CNhs13031 DRZ012781 DRZ014164
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

CNhs13031

00
10.823
100
1000
10000
10010.0131
1002-0.0479
10030.373
10040
10050.0209
10060.65
1007-0.216
10080
1009-0.19
101-0.0664
10100
10110.918
10120.582
10130.0875
10140
1015-0.00509
1016-0.151
10170
10180
10190
1020
10200.582
10210
1022-0.0704
10230
1024-0.113
10250
10260
10270.46
10280
10290.423
103-0.0829
10300
1031-0.568
10320.118
10330
10340
10350
1036-0.0705
10370
10380.0309
1039-0.0381
1040
1040-0.257
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: CNhs13031

Jaspar motifP-value
MA0002.20.0325
MA0003.10.268
MA0004.10.574
MA0006.10.0924
MA0007.10.329
MA0009.10.927
MA0014.10.563
MA0017.11.26537e-6
MA0018.20.0139
MA0019.10.0905
MA0024.10.0208
MA0025.10.532
MA0027.10.064
MA0028.10.034
MA0029.10.923
MA0030.10.702
MA0031.10.0111
MA0035.20.0182
MA0038.10.903
MA0039.20.00321
MA0040.10.073
MA0041.10.436
MA0042.10.514
MA0043.10.763
MA0046.13.35247e-10
MA0047.21.98753e-4
MA0048.10.0635
MA0050.11.6123e-5
MA0051.14.8664e-4
MA0052.10.656
MA0055.10.0136
MA0057.10.468
MA0058.10.332
MA0059.10.277
MA0060.10.072
MA0061.10.0673
MA0062.21.28165e-4
MA0065.21.37103e-6
MA0066.10.124
MA0067.10.553
MA0068.10.153
MA0069.10.0446
MA0070.10.841
MA0071.10.0403
MA0072.10.121
MA0073.10.821
MA0074.10.108
MA0076.10.0683
MA0077.10.654
MA0078.10.994
MA0079.20.985
MA0080.21.86874e-10
MA0081.10.151
MA0083.10.00181
MA0084.10.672
MA0087.10.428
MA0088.10.342
MA0090.10.0693
MA0091.10.26
MA0092.10.318
MA0093.10.553
MA0099.24.35974e-4
MA0100.10.381
MA0101.10.0163
MA0102.20.271
MA0103.10.269
MA0104.20.864
MA0105.10.101
MA0106.10.0892
MA0107.10.0445
MA0108.24.69382e-5
MA0111.10.795
MA0112.20.00128
MA0113.10.215
MA0114.14.0741e-6
MA0115.15.94291e-4
MA0116.10.178
MA0117.10.793
MA0119.10.113
MA0122.10.71
MA0124.10.778
MA0125.10.443
MA0131.10.682
MA0135.10.185
MA0136.17.03549e-12
MA0137.20.073
MA0138.20.00514
MA0139.10.478
MA0140.10.00542
MA0141.10.00134
MA0142.10.459
MA0143.10.611
MA0144.10.0514
MA0145.10.071
MA0146.10.0114
MA0147.10.922
MA0148.11.15082e-4
MA0149.10.347
MA0150.10.15
MA0152.10.995
MA0153.12.10701e-10
MA0154.10.0751
MA0155.10.336
MA0156.17.38329e-12
MA0157.10.0213
MA0159.10.00855
MA0160.10.00472
MA0162.10.166
MA0163.10.00372
MA0164.10.938
MA0258.10.0293
MA0259.10.708



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: CNhs13031

Novel motifP-value
10.421
100.126
1000.462
1010.414
1020.834
1030.145
1040.992
1050.412
1060.0412
1070.102
1080.393
1090.00311
110.0557
1100.064
1110.395
1120.0123
1130.366
1140.587
1150.86
1160.368
1170.00979
1180.595
1190.185
120.583
1200.866
1210.111
1220.996
1230.00133
1240.0457
1250.985
1260.0446
1270.606
1280.0569
1290.475
135.10364e-9
1300.0285
1310.352
1320.558
1330.329
1340.0969
1350.275
1360.00204
1370.442
1380.731
1390.839
140.794
1400.668
1410.709
1420.662
1430.508
1440.655
1452.98394e-4
1460.202
1470.0637
1480.384
1490.405
150.218
1500.0346
1510.788
1520.0614
1530.664
1540.953
1550.567
1561.33525e-8
1570.234
1580.497
1590.224
1600.316
1610.0609
1620.687
1630.898
1640.144
1650.115
1660.537
1670.221
1680.592
1690.00412
170.0546
180.85
190.0522
20.986
200.076
210.192
220.0786
230.667
240.0194
250.918
267.02705e-7
270.595
280.586
290.0565
30.0584
300.875
310.744
320.796
330.139
340.525
350.441
360.552
370.0166
380.379
390.195
40.226
400.121
410.637
420.202
430.117
440.784
450.51
460.243
470.354
480.305
490.338
50.371
500.2
510.702
520.172
530.723
540.96
550.967
560.45
570.79
580.415
590.12
60.943
600.0258
610.0278
620.284
630.138
640.678
650.23
660.489
670.761
680.201
690.241
70.0182
700.343
710.0137
720.39
730.0168
740.632
750.0602
760.65
770.366
780.0017
790.749
80.192
800.775
810.685
820.394
830.0449
840.771
850.234
860.17
870.00208
880.541
890.88
90.321
900.637
910.437
920.522
930.595
940.748
950.0206
960.57
970.91
980.504
990.392



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: CNhs13031


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)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000316 (mouse neonate N15 sample)
0011268 (mouse visual cortex from wildtype- neonate N15 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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