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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005326
|DRA_sample_Accession=CAGE@SAMD00005326
|accession_numbers=CAGE;DRX009135;DRR010009;DRZ001434;DRZ002817
|accession_numbers=CAGE;DRX009135;DRR010009;DRZ001434;DRZ002817;DRZ012784;DRZ014167
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;10349
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10349
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;10349
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10349
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor5.CNhs13820.10349-105D7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor5.CNhs13820.10349-105D7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor5.CNhs13820.10349-105D7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor5.CNhs13820.10349-105D7.mm10.nobarcode.ctss.bed.gz
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10349-105D7;search_select_hide=table117:10349-105D7
}}
}}

Latest revision as of 13:58, 3 June 2020


Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13820
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 typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005326
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13820 CAGE DRX009135 DRR010009
Accession ID Mm9

Library idBAMCTSS
CNhs13820 DRZ001434 DRZ002817
Accession ID Mm10

Library idBAMCTSS
CNhs13820 DRZ012784 DRZ014167
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

CNhs13820

00
10.823
100
1000.0307
10000.0287
10010.0534
1002-0.0804
10030.468
10040.0689
10050.0894
10060.565
1007-0.193
10080
1009-0.193
101-0.104
10100
10110.89
10120.51
10130.109
10140.0689
1015-0.053
1016-0.031
10170
10180
10190
1020
10200.835
10210
1022-0.0704
10230
1024-0.0113
10250
10260
10270.345
10280
10290.0444
103-0.0788
10300
1031-0.547
10320.115
10330.105
10340
10350
1036-0.111
10370
10380.0388
10390.0887
1040
1040-0.39
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: CNhs13820

Jaspar motifP-value
MA0002.20.00343
MA0003.10.216
MA0004.10.55
MA0006.10.105
MA0007.10.482
MA0009.10.64
MA0014.10.621
MA0017.15.22257e-7
MA0018.20.0189
MA0019.10.076
MA0024.10.0679
MA0025.10.884
MA0027.10.0626
MA0028.10.0429
MA0029.10.779
MA0030.10.22
MA0031.10.0112
MA0035.20.0139
MA0038.10.599
MA0039.20.00286
MA0040.10.0415
MA0041.10.543
MA0042.10.667
MA0043.10.607
MA0046.17.46245e-11
MA0047.24.17909e-4
MA0048.10.166
MA0050.10.00109
MA0051.10.00925
MA0052.10.443
MA0055.10.0352
MA0057.10.375
MA0058.10.339
MA0059.10.346
MA0060.10.0503
MA0061.10.0572
MA0062.21.71301e-4
MA0065.23.36869e-7
MA0066.10.0811
MA0067.10.533
MA0068.10.59
MA0069.10.0752
MA0070.10.758
MA0071.10.0436
MA0072.10.155
MA0073.10.836
MA0074.10.134
MA0076.10.0842
MA0077.10.949
MA0078.10.719
MA0079.20.997
MA0080.23.51128e-10
MA0081.10.156
MA0083.10.00771
MA0084.10.836
MA0087.10.429
MA0088.10.263
MA0090.10.0469
MA0091.10.301
MA0092.10.339
MA0093.10.554
MA0099.29.70758e-5
MA0100.10.285
MA0101.10.0363
MA0102.20.384
MA0103.10.19
MA0104.20.948
MA0105.10.0608
MA0106.10.0938
MA0107.10.0604
MA0108.28.90945e-4
MA0111.10.799
MA0112.20.00108
MA0113.10.221
MA0114.11.65753e-6
MA0115.16.38924e-5
MA0116.10.116
MA0117.10.834
MA0119.10.114
MA0122.10.812
MA0124.10.85
MA0125.10.501
MA0131.10.93
MA0135.10.129
MA0136.18.6103e-10
MA0137.20.223
MA0138.20.00718
MA0139.10.452
MA0140.14.94393e-4
MA0141.10.0012
MA0142.10.372
MA0143.10.514
MA0144.10.097
MA0145.10.0512
MA0146.10.0119
MA0147.10.982
MA0148.19.16556e-4
MA0149.10.351
MA0150.10.0684
MA0152.10.397
MA0153.12.80728e-11
MA0154.10.0358
MA0155.10.298
MA0156.11.09515e-10
MA0157.10.0425
MA0159.10.00246
MA0160.10.00123
MA0162.10.183
MA0163.10.00363
MA0164.10.659
MA0258.10.0359
MA0259.10.694



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: CNhs13820

Novel motifP-value
10.363
100.137
1000.53
1010.74
1020.943
1030.0991
1040.957
1050.436
1060.079
1070.152
1080.565
1090.00372
110.102
1100.0662
1110.479
1120.0125
1130.519
1140.468
1150.761
1160.391
1170.00746
1180.516
1190.0874
120.605
1200.887
1210.0472
1220.783
1230.0145
1240.129
1250.858
1260.0329
1270.576
1280.0595
1290.37
131.10358e-7
1300.0695
1310.245
1320.569
1330.259
1340.127
1350.589
1360.00752
1370.549
1380.859
1390.708
140.647
1400.694
1410.737
1420.833
1430.515
1440.58
1450.00116
1460.126
1470.0974
1480.711
1490.279
150.182
1500.0528
1510.663
1520.0979
1530.996
1540.743
1550.415
1566.98886e-32
1570.264
1580.135
1590.754
1600.302
1610.0526
1620.718
1630.67
1640.133
1650.185
1660.642
1670.236
1680.389
1690.00375
170.0738
180.995
190.0634
20.766
200.165
210.31
220.0693
230.297
240.00632
250.785
264.31847e-6
270.745
280.612
290.0627
30.0652
300.838
310.826
320.771
330.2
340.468
350.63
360.594
370.0201
380.177
390.354
40.155
400.123
410.417
420.208
430.137
440.541
450.466
460.263
470.423
480.329
490.32
50.518
500.197
510.682
520.172
530.87
540.887
550.979
560.45
570.814
580.301
590.0874
60.961
600.0267
610.0606
620.237
630.117
640.615
650.151
660.563
670.715
680.321
690.214
70.0129
700.336
710.0182
720.349
730.0305
740.682
750.0627
760.989
770.252
780.00175
790.606
80.287
800.867
810.897
820.285
830.0458
840.579
850.152
860.165
870.00584
880.501
890.711
90.315
900.636
910.44
920.497
930.531
940.872
950.0237
960.452
970.932
980.254
990.499



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: CNhs13820


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)

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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