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|is_obsolete=
|is_obsolete=
|library_id=CNhs13032
|library_id=CNhs13032
|library_ids=CNhs13032
|name=visual cortex - wildtype, neonate N15, donor2
|name=visual cortex - wildtype, neonate N15, donor2
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:16, 25 October 2013


Name:visual cortex - wildtype, neonate N15, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs13032
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM: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  DRS008996
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13032 CAGE DRX009133 DRR010007
Accession ID Mm9

Library idBAMCTSS
CNhs13032 DRZ001432 DRZ002815
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs13032

00
10.815
100
1000
10000.0919
1001-0.00227
1002-0.0941
10030.409
10040
10050
10060.603
1007-0.164
10080
1009-0.19
101-0.0675
10100
10110.941
10120.651
10130.119
10140
10150.0837
1016-0.0769
10170
10180
10190
1020
10200.454
10210
1022-0.124
10230
1024-0.0899
1025-0.0611
10260
10270.519
10280
10290.107
103-0.0848
10300
1031-0.627
10320.107
10330.137
10340
10350
1036-0.183
10370
1038-0.0774
1039-0.02
1040
1040-0.457
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: CNhs13032

Jaspar motifP-value
MA0002.20.0281
MA0003.10.282
MA0004.10.515
MA0006.10.105
MA0007.10.432
MA0009.10.878
MA0014.10.526
MA0017.11.59959e-7
MA0018.20.00938
MA0019.10.132
MA0024.10.0292
MA0025.10.439
MA0027.10.104
MA0028.10.0295
MA0029.10.548
MA0030.10.427
MA0031.10.00547
MA0035.20.0151
MA0038.10.803
MA0039.20.00253
MA0040.10.0705
MA0041.10.264
MA0042.10.504
MA0043.10.668
MA0046.11.32485e-9
MA0047.22.93056e-4
MA0048.10.0526
MA0050.12.92095e-6
MA0051.11.35642e-4
MA0052.10.796
MA0055.10.00973
MA0057.10.491
MA0058.10.327
MA0059.10.254
MA0060.10.0377
MA0061.10.0657
MA0062.28.11293e-5
MA0065.27.78532e-7
MA0066.10.106
MA0067.10.61
MA0068.10.173
MA0069.10.124
MA0070.10.97
MA0071.10.0446
MA0072.10.115
MA0073.10.824
MA0074.10.164
MA0076.10.0617
MA0077.10.782
MA0078.10.958
MA0079.20.91
MA0080.21.31688e-10
MA0081.10.177
MA0083.17.4769e-4
MA0084.10.628
MA0087.10.711
MA0088.10.303
MA0090.10.14
MA0091.10.245
MA0092.10.265
MA0093.10.529
MA0099.26.06593e-4
MA0100.10.354
MA0101.10.0226
MA0102.20.17
MA0103.10.258
MA0104.20.936
MA0105.10.0951
MA0106.10.0809
MA0107.10.0512
MA0108.27.21059e-5
MA0111.10.693
MA0112.29.7593e-4
MA0113.10.244
MA0114.11.56758e-6
MA0115.11.54161e-4
MA0116.10.152
MA0117.10.785
MA0119.10.0981
MA0122.10.633
MA0124.10.947
MA0125.10.19
MA0131.10.76
MA0135.10.276
MA0136.17.48477e-12
MA0137.20.0877
MA0138.20.00476
MA0139.10.432
MA0140.10.00149
MA0141.10.00118
MA0142.10.301
MA0143.10.783
MA0144.10.0501
MA0145.10.0726
MA0146.10.00922
MA0147.10.988
MA0148.14.11275e-4
MA0149.10.33
MA0150.10.141
MA0152.10.83
MA0153.14.37855e-10
MA0154.10.0501
MA0155.10.313
MA0156.15.24508e-11
MA0157.10.00695
MA0159.10.00401
MA0160.10.00195
MA0162.10.182
MA0163.10.00473
MA0164.10.873
MA0258.10.0296
MA0259.10.827



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: CNhs13032

Novel motifP-value
10.37
100.104
1000.428
1010.35
1020.793
1030.198
1040.977
1050.493
1060.0501
1070.0966
1080.406
1090.00303
110.0749
1100.0536
1110.35
1120.0111
1130.362
1140.615
1150.919
1160.303
1170.0067
1180.579
1190.136
120.714
1200.885
1210.135
1220.812
1233.91669e-4
1240.0423
1250.973
1260.024
1270.557
1280.0535
1290.332
134.64296e-9
1300.0363
1310.412
1320.467
1330.335
1340.0652
1350.137
1360.00363
1370.694
1380.669
1390.948
140.752
1400.205
1410.954
1420.908
1430.583
1440.563
1451.62379e-4
1460.211
1470.0829
1480.509
1490.577
150.289
1500.0359
1510.746
1520.0745
1530.928
1540.84
1550.425
1561.28279e-10
1570.253
1580.231
1590.376
1600.354
1610.0655
1620.6
1630.988
1640.0966
1650.129
1660.511
1670.321
1680.651
1690.00321
170.0661
180.834
190.0535
20.96
200.0509
210.192
220.075
230.596
240.0214
250.882
264.94484e-7
270.585
280.638
290.0502
30.0601
300.976
310.795
320.783
330.209
340.488
350.46
360.549
370.0182
380.328
390.208
40.246
400.112
410.585
420.232
430.13
440.886
450.542
460.27
470.418
480.344
490.326
50.422
500.166
510.773
520.192
530.599
540.969
550.732
560.497
570.812
580.443
590.119
60.969
600.028
610.029
620.336
630.109
640.643
650.27
660.407
670.912
680.39
690.239
70.0122
700.309
710.0121
720.527
730.0224
740.755
750.0738
760.771
770.362
780.00333
790.581
80.214
800.543
810.635
820.501
830.0327
840.892
850.269
860.181
870.00734
880.5
890.815
90.388
900.49
910.289
920.615
930.437
940.838
950.0179
960.673
970.918
980.47
990.485



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: CNhs13032


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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