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FF:10242-104A8

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13038
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 60-70
sexmale
ageP60-70
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  SAMD00004869
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13038 CAGE DRX009140 DRR010014
Accession ID Mm9

Library idBAMCTSS
CNhs13038 DRZ001439 DRZ002822
Accession ID Mm10

Library idBAMCTSS
CNhs13038 DRZ012789 DRZ014172
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

CNhs13038

00
10.838
100
1000
10000
10010.0345
1002-0.116
10030.397
10040
10050
10060.62
1007-0.246
10080
1009-0.0938
101-0.0304
10100
10110.938
10120.373
10130.186
1014-0.0874
1015-0.112
1016-0.23
10170
10180
10190
1020
10200.449
10210
1022-0.0704
10230
1024-0.0269
1025-0.0194
10260
10270.388
10280
10290.273
103-0.0848
10300
1031-0.661
10320.196
1033-0.0013
10340
10350
1036-0.292
10370
10380.0919
10390.00256
1040
1040-0.139
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: CNhs13038

Jaspar motifP-value
MA0002.20.0187
MA0003.10.253
MA0004.10.573
MA0006.10.0852
MA0007.10.471
MA0009.10.984
MA0014.10.693
MA0017.19.53978e-7
MA0018.20.00112
MA0019.10.129
MA0024.10.0276
MA0025.10.0107
MA0027.10.0348
MA0028.10.0656
MA0029.10.814
MA0030.10.345
MA0031.10.024
MA0035.20.0129
MA0038.10.887
MA0039.20.00256
MA0040.10.0374
MA0041.10.336
MA0042.10.404
MA0043.10.139
MA0046.11.32877e-10
MA0047.23.48871e-4
MA0048.10.0488
MA0050.16.60438e-6
MA0051.10.00135
MA0052.10.966
MA0055.10.00731
MA0057.10.501
MA0058.10.327
MA0059.10.257
MA0060.10.0209
MA0061.10.0416
MA0062.24.24129e-4
MA0065.22.83918e-6
MA0066.10.0701
MA0067.10.288
MA0068.10.223
MA0069.10.138
MA0070.10.659
MA0071.10.0261
MA0072.10.0848
MA0073.10.839
MA0074.10.131
MA0076.10.136
MA0077.10.94
MA0078.10.978
MA0079.20.916
MA0080.21.31596e-10
MA0081.10.196
MA0083.10.00876
MA0084.10.229
MA0087.10.679
MA0088.10.27
MA0090.10.14
MA0091.10.231
MA0092.10.32
MA0093.10.588
MA0099.20.00565
MA0100.10.422
MA0101.10.0114
MA0102.20.208
MA0103.10.4
MA0104.20.913
MA0105.10.0582
MA0106.10.0449
MA0107.10.0232
MA0108.23.75612e-5
MA0111.10.669
MA0112.20.00231
MA0113.10.258
MA0114.12.64155e-6
MA0115.15.29622e-4
MA0116.10.132
MA0117.10.637
MA0119.10.0842
MA0122.10.678
MA0124.10.841
MA0125.10.319
MA0131.10.695
MA0135.10.23
MA0136.15.42514e-13
MA0137.20.305
MA0138.20.00278
MA0139.10.626
MA0140.10.00125
MA0141.10.00147
MA0142.10.356
MA0143.10.548
MA0144.10.119
MA0145.10.0903
MA0146.10.0112
MA0147.10.926
MA0148.11.59235e-4
MA0149.10.31
MA0150.10.319
MA0152.10.634
MA0153.15.34461e-10
MA0154.10.0543
MA0155.10.349
MA0156.15.55586e-11
MA0157.10.0542
MA0159.10.00625
MA0160.10.0042
MA0162.10.174
MA0163.10.00444
MA0164.10.965
MA0258.10.0417
MA0259.10.837



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: CNhs13038

Novel motifP-value
10.396
100.102
1000.488
1010.557
1020.879
1030.095
1040.992
1050.53
1060.0664
1070.142
1080.439
1090.00237
110.1
1100.0615
1110.57
1120.0241
1130.359
1140.653
1150.852
1160.25
1170.00477
1180.556
1190.308
120.761
1200.741
1210.194
1220.876
1238.76756e-4
1240.014
1250.342
1260.0368
1270.519
1280.0611
1290.402
138.33679e-9
1300.0537
1310.623
1320.584
1330.31
1340.0758
1350.483
1360.00626
1370.565
1380.725
1390.404
140.841
1400.251
1410.956
1420.704
1430.515
1440.569
1459.04384e-5
1460.165
1470.0908
1480.391
1490.506
150.267
1500.0353
1510.832
1520.0701
1530.947
1540.885
1550.411
1560.0196
1570.171
1580.284
1590.451
1600.321
1610.089
1620.473
1630.821
1640.193
1650.129
1660.497
1670.194
1680.622
1690.00566
170.0802
180.87
190.0526
20.841
200.0367
210.224
220.0923
230.755
240.00797
250.948
261.06538e-6
270.403
280.7
290.044
30.0523
300.959
310.82
320.779
330.241
340.391
350.497
360.601
370.0207
380.423
390.21
40.178
400.115
410.598
420.165
430.14
440.93
450.534
460.254
470.594
480.361
490.364
50.353
500.141
510.759
520.181
530.541
540.951
550.955
560.475
570.918
580.436
590.105
60.961
600.0385
610.0335
620.351
630.123
640.679
650.438
660.52
670.827
680.253
690.234
70.0181
700.372
710.0142
720.517
730.021
740.764
750.0529
760.845
770.278
780.00263
790.554
80.166
800.678
810.699
820.412
830.0251
840.861
850.173
860.215
870.0151
880.673
890.899
90.353
900.582
910.154
920.52
930.497
940.887
950.0162
960.605
970.836
980.342
990.475



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: CNhs13038


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)
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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000315 (mouse neonate N60-70 sample)
0011270 (mouse visual cortex from wildtype- neonate N60-70 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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