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FF:10243-104A9

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13039
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  SAMD00004914
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13039 CAGE DRX009141 DRR010015
Accession ID Mm9

Library idBAMCTSS
CNhs13039 DRZ001440 DRZ002823
Accession ID Mm10

Library idBAMCTSS
CNhs13039 DRZ012790 DRZ014173
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

CNhs13039

00
10.834
100
1000
1000-0.0355
10010.0737
1002-0.0873
10030.399
10040
10050
10060.668
1007-0.174
10080
1009-0.19
101-0.104
10100
10110.884
10120.487
10130.092
10140
1015-0.205
1016-0.37
10170
10180
10190
1020
10200.487
10210
1022-0.0464
10230
10240
10250
10260
10270.261
10280
10290.126
103-0.0848
10300
1031-0.528
10320.125
10330
10340
10350
1036-0.183
10370
10380.0983
10390.0942
1040
1040-0.134
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: CNhs13039

Jaspar motifP-value
MA0002.20.0239
MA0003.10.239
MA0004.10.614
MA0006.10.0955
MA0007.10.365
MA0009.10.824
MA0014.10.614
MA0017.16.06206e-7
MA0018.20.00207
MA0019.10.084
MA0024.10.0184
MA0025.10.0288
MA0027.10.0711
MA0028.10.0316
MA0029.10.8
MA0030.10.422
MA0031.10.0273
MA0035.20.0156
MA0038.10.454
MA0039.20.00224
MA0040.10.0475
MA0041.10.438
MA0042.10.416
MA0043.10.132
MA0046.19.4658e-11
MA0047.23.35562e-4
MA0048.10.0718
MA0050.15.64718e-6
MA0051.14.69052e-4
MA0052.10.676
MA0055.10.00975
MA0057.10.495
MA0058.10.38
MA0059.10.283
MA0060.10.00427
MA0061.10.0409
MA0062.21.28257e-4
MA0065.23.87464e-6
MA0066.10.0879
MA0067.10.394
MA0068.10.166
MA0069.10.0976
MA0070.10.957
MA0071.10.0621
MA0072.10.149
MA0073.10.81
MA0074.10.185
MA0076.10.0694
MA0077.10.928
MA0078.10.967
MA0079.20.924
MA0080.22.64054e-10
MA0081.10.175
MA0083.10.00186
MA0084.10.347
MA0087.10.682
MA0088.10.223
MA0090.10.174
MA0091.10.444
MA0092.10.285
MA0093.10.639
MA0099.20.00505
MA0100.10.313
MA0101.10.0104
MA0102.20.358
MA0103.10.458
MA0104.20.924
MA0105.10.0479
MA0106.10.0541
MA0107.10.0195
MA0108.26.18179e-6
MA0111.10.592
MA0112.20.00162
MA0113.10.129
MA0114.14.24064e-6
MA0115.14.38193e-4
MA0116.10.177
MA0117.10.751
MA0119.10.0808
MA0122.10.789
MA0124.10.89
MA0125.10.46
MA0131.10.669
MA0135.10.0966
MA0136.11.09683e-12
MA0137.20.128
MA0138.20.00883
MA0139.10.573
MA0140.10.00163
MA0141.10.00255
MA0142.10.379
MA0143.10.406
MA0144.10.11
MA0145.10.0975
MA0146.10.0108
MA0147.10.952
MA0148.12.75743e-4
MA0149.10.23
MA0150.10.177
MA0152.10.452
MA0153.15.12675e-10
MA0154.10.0765
MA0155.10.301
MA0156.17.41177e-12
MA0157.10.0288
MA0159.10.00858
MA0160.10.00535
MA0162.10.189
MA0163.10.00608
MA0164.10.841
MA0258.10.0547
MA0259.10.856



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: CNhs13039

Novel motifP-value
10.386
100.0881
1000.483
1010.467
1020.978
1030.0839
1040.969
1050.603
1060.0677
1070.258
1080.351
1090.00251
110.103
1100.051
1110.369
1120.00969
1130.399
1140.748
1150.922
1160.245
1170.00431
1180.55
1190.22
120.821
1200.739
1210.159
1220.99
1233.99086e-4
1240.0289
1250.528
1260.0385
1270.602
1280.0747
1290.306
135.06591e-9
1300.0423
1310.423
1320.532
1330.31
1340.0645
1350.298
1360.0144
1370.483
1380.703
1390.955
140.941
1400.379
1410.862
1420.655
1430.566
1440.557
1457.99265e-5
1460.126
1470.0755
1480.56
1490.537
150.293
1500.0463
1510.785
1520.0681
1530.989
1540.852
1550.331
1560.127
1570.192
1580.351
1590.354
1600.242
1610.107
1620.623
1630.907
1640.145
1650.0503
1660.644
1670.168
1680.676
1690.00476
170.074
180.7
190.0641
20.894
200.0443
210.258
220.0854
230.814
240.00747
250.906
262.27727e-7
270.446
280.631
290.0416
30.0516
300.979
310.754
320.793
330.232
340.493
350.42
360.419
370.0194
380.525
390.225
40.352
400.104
410.551
420.19
430.149
440.771
450.576
460.271
470.489
480.339
490.393
50.28
500.146
510.754
520.159
530.599
540.936
550.971
560.494
570.877
580.431
590.152
60.999
600.0309
610.0318
620.353
630.121
640.708
650.48
660.451
670.953
680.196
690.251
70.0143
700.45
710.00754
720.587
730.023
740.866
750.0558
760.844
770.38
780.00115
790.657
80.173
800.776
810.66
820.368
830.0472
840.967
850.21
860.204
870.0118
880.591
890.968
90.377
900.553
910.184
920.527
930.311
940.941
950.0173
960.633
970.921
980.608
990.417



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: CNhs13039


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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