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FF:10241-104A7

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13037
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  SAMD00005563
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13037 CAGE DRX009139 DRR010013
Accession ID Mm9

Library idBAMCTSS
CNhs13037 DRZ001438 DRZ002821
Accession ID Mm10

Library idBAMCTSS
CNhs13037 DRZ012788 DRZ014171
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

CNhs13037

00
10.836
100
1000
10000
10010.0395
1002-0.0639
10030.287
10040
10050
10060.598
1007-0.101
10080
1009-0.19
101-0.0853
10100
10110.864
10120.279
10130.169
1014-0.0874
1015-0.0569
1016-0.126
10170
10180
10190
1020
10200.447
10210
1022-0.0704
10230
1024-0.0899
10250
10260
10270.33
10280
10290.164
103-0.0829
10300
1031-0.54
10320.188
1033-0.00214
10340
10350
1036-0.183
10370
10380.0222
10390.025
1040
1040-0.216
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: CNhs13037

Jaspar motifP-value
MA0002.20.0138
MA0003.10.251
MA0004.10.51
MA0006.10.0859
MA0007.10.472
MA0009.10.783
MA0014.10.687
MA0017.17.82949e-7
MA0018.20.00273
MA0019.10.0938
MA0024.10.0223
MA0025.10.0225
MA0027.10.0673
MA0028.10.0592
MA0029.10.933
MA0030.10.401
MA0031.10.0326
MA0035.20.0202
MA0038.10.727
MA0039.20.00242
MA0040.10.0568
MA0041.10.354
MA0042.10.496
MA0043.10.303
MA0046.18.07743e-11
MA0047.27.48377e-4
MA0048.10.0546
MA0050.12.7057e-5
MA0051.16.47204e-4
MA0052.10.945
MA0055.10.00718
MA0057.10.469
MA0058.10.302
MA0059.10.263
MA0060.10.029
MA0061.10.0453
MA0062.23.05115e-4
MA0065.21.75335e-6
MA0066.10.104
MA0067.10.495
MA0068.10.248
MA0069.10.0608
MA0070.10.921
MA0071.10.0555
MA0072.10.199
MA0073.10.785
MA0074.10.123
MA0076.10.113
MA0077.10.858
MA0078.10.969
MA0079.20.966
MA0080.22.90366e-10
MA0081.10.238
MA0083.10.00597
MA0084.10.475
MA0087.10.558
MA0088.10.32
MA0090.10.223
MA0091.10.295
MA0092.10.241
MA0093.10.51
MA0099.20.00263
MA0100.10.401
MA0101.10.00952
MA0102.20.175
MA0103.10.403
MA0104.20.889
MA0105.10.0601
MA0106.10.0521
MA0107.10.0234
MA0108.26.07477e-6
MA0111.10.748
MA0112.20.00201
MA0113.10.26
MA0114.12.27965e-6
MA0115.13.39321e-4
MA0116.10.179
MA0117.10.79
MA0119.10.164
MA0122.10.595
MA0124.10.859
MA0125.10.253
MA0131.10.723
MA0135.10.23
MA0136.11.82808e-12
MA0137.20.194
MA0138.29.50974e-4
MA0139.10.493
MA0140.10.00144
MA0141.10.00328
MA0142.10.388
MA0143.10.509
MA0144.10.0866
MA0145.10.0824
MA0146.10.00924
MA0147.10.882
MA0148.12.67634e-4
MA0149.10.301
MA0150.10.198
MA0152.10.987
MA0153.12.19889e-12
MA0154.10.0813
MA0155.10.36
MA0156.11.08325e-10
MA0157.10.037
MA0159.10.00897
MA0160.10.00469
MA0162.10.184
MA0163.10.00541
MA0164.10.735
MA0258.10.0479
MA0259.10.773



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: CNhs13037

Novel motifP-value
10.303
100.0994
1000.447
1010.521
1020.922
1030.153
1040.901
1050.59
1060.0574
1070.19
1080.476
1090.00257
110.104
1100.0622
1110.523
1120.0138
1130.37
1140.843
1150.814
1160.35
1170.00491
1180.548
1190.216
120.751
1200.753
1210.16
1220.958
1239.70657e-4
1240.043
1250.736
1260.0449
1270.483
1280.0483
1290.364
134.25523e-9
1300.0305
1310.502
1320.433
1330.192
1340.0757
1350.399
1360.00704
1370.498
1380.533
1390.489
140.881
1400.37
1410.861
1420.886
1430.556
1440.648
1451.33291e-4
1460.184
1470.113
1480.464
1490.504
150.251
1500.0519
1510.827
1520.0664
1530.773
1540.909
1550.42
1561.33485e-6
1570.195
1580.232
1590.4
1600.285
1610.0846
1620.5
1630.983
1640.107
1650.118
1660.661
1670.195
1680.577
1690.00502
170.0705
180.858
190.0564
20.855
200.051
210.153
220.0879
230.702
240.0141
250.881
261.62361e-6
270.452
280.639
290.0387
30.0558
300.996
310.821
320.79
330.232
340.432
350.482
360.578
370.018
380.41
390.26
40.155
400.116
410.586
420.187
430.138
440.844
450.528
460.232
470.558
480.365
490.381
50.43
500.155
510.816
520.174
530.642
540.92
550.811
560.493
570.86
580.398
590.134
60.928
600.0397
610.0344
620.345
630.129
640.651
650.39
660.476
670.765
680.53
690.127
70.0154
700.383
710.0124
720.522
730.0177
740.969
750.0542
760.756
770.368
780.00262
790.35
80.151
800.758
810.834
820.427
830.0185
840.982
850.231
860.194
870.0165
880.559
890.976
90.363
900.456
910.146
920.423
930.371
940.87
950.0126
960.47
970.838
980.364
990.51



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: CNhs13037


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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