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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;345
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;345
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;345
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;345
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.ctss.bed.gz

Revision as of 18:31, 4 August 2017


Name:eyeball, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs11016
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage12 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005612
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11016 CAGE DRX008955 DRR009829
Accession ID Mm9

Library idBAMCTSS
CNhs11016 DRZ001254 DRZ002637
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

CNhs11016

00
10.0257
100
1000.1
1000-0.0355
10010.0588
10020.354
1003-0.104
10040.654
1005-0.0978
1006-0.0752
10070.142
10080
1009-0.0469
1010.158
10100
10110.0522
10120
1013-0.149
10140.267
10150.343
10160.222
10170
10180
10190
1020
10200
10210.0531
1022-0.0709
10230
1024-0.0367
10250
10260
10270.262
10280
10290.203
103-0.0136
10300
10310.199
1032-0.141
10330.0531
10340
10350
10360.129
10370
1038-0.0941
1039-0.097
1040
10400.0257
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: CNhs11016

Jaspar motifP-value
MA0002.21.87475e-5
MA0003.10.108
MA0004.10.908
MA0006.10.282
MA0007.10.334
MA0009.10.221
MA0014.10.196
MA0017.12.45987e-4
MA0018.20.499
MA0019.10.834
MA0024.11.25523e-4
MA0025.10.0127
MA0027.10.12
MA0028.10.184
MA0029.10.623
MA0030.10.0403
MA0031.16.71054e-4
MA0035.20.00205
MA0038.10.00372
MA0039.20.00181
MA0040.10.0347
MA0041.10.198
MA0042.10.329
MA0043.10.122
MA0046.11.3655e-29
MA0047.22.83134e-5
MA0048.10.21
MA0050.12.90774e-7
MA0051.12.32766e-5
MA0052.11.95362e-6
MA0055.10.0769
MA0057.10.076
MA0058.10.705
MA0059.10.314
MA0060.12.5449e-13
MA0061.10.0645
MA0062.20.638
MA0065.21.91768e-5
MA0066.10.312
MA0067.10.53
MA0068.10.367
MA0069.10.102
MA0070.10.781
MA0071.10.532
MA0072.10.364
MA0073.10.166
MA0074.10.597
MA0076.10.117
MA0077.10.00613
MA0078.10.39
MA0079.20.198
MA0080.24.76839e-12
MA0081.10.256
MA0083.10.0336
MA0084.10.757
MA0087.10.285
MA0088.10.514
MA0090.10.42
MA0091.10.456
MA0092.10.324
MA0093.10.869
MA0099.21.12308e-6
MA0100.10.714
MA0101.10.239
MA0102.20.197
MA0103.10.00351
MA0104.20.235
MA0105.10.0347
MA0106.10.485
MA0107.10.101
MA0108.20.613
MA0111.10.549
MA0112.21.426e-4
MA0113.10.431
MA0114.14.1306e-4
MA0115.10.0996
MA0116.10.0346
MA0117.10.36
MA0119.10.00512
MA0122.10.855
MA0124.10.277
MA0125.10.0936
MA0131.10.343
MA0135.10.552
MA0136.12.37768e-8
MA0137.20.156
MA0138.21.61872e-4
MA0139.10.125
MA0140.10.029
MA0141.10.00557
MA0142.10.127
MA0143.12.00473e-4
MA0144.10.0895
MA0145.10.00878
MA0146.10.299
MA0147.10.368
MA0148.19.75145e-6
MA0149.10.0289
MA0150.10.013
MA0152.10.153
MA0153.14.85168e-19
MA0154.10.0015
MA0155.10.755
MA0156.10.00237
MA0157.10.00419
MA0159.10.0318
MA0160.10.0237
MA0162.10.874
MA0163.10.0542
MA0164.10.672
MA0258.10.00477
MA0259.10.501



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: CNhs11016

Novel motifP-value
10.127
100.378
1000.656
1010.68
1020.68
1030.118
1040.947
1050.129
1060.00682
1070.0688
1080.668
1090.117
110.113
1100.248
1110.0514
1120.0516
1130.54
1140.0536
1150.822
1160.556
1170.631
1180.875
1190.0425
120.853
1200.46
1210.808
1220.895
1230.156
1240.142
1250.211
1260.498
1270.12
1280.0981
1290.161
130.231
1300.903
1310.148
1320.247
1330.773
1340.623
1350.188
1360.783
1370.572
1380.583
1390.0207
140.347
1400.188
1410.0303
1420.312
1430.467
1440.983
1450.299
1460.192
1470.375
1480.297
1490.0437
150.0806
1500.721
1510.126
1520.0255
1530.637
1540.977
1550.771
1560.47
1570.674
1580.604
1590.872
1600.737
1610.748
1620.802
1630.0855
1640.102
1650.0851
1660.469
1670.914
1680.339
1690.00397
170.0422
180.56
190.183
20.285
200.54
210.639
220.215
230.0546
240.365
250.472
260.306
270.348
280.373
290.586
30.292
300.527
310.582
320.122
330.806
340.604
350.753
360.294
370.0638
380.174
390.652
40.333
400.227
410.44
420.644
430.154
440.125
450.308
460.322
470.192
480.179
490.195
50.145
500.889
510.571
520.151
530.489
540.35
550.657
560.305
570.662
580.242
590.0293
60.529
600.0487
610.854
620.103
630.0976
640.464
650.0789
660.583
670.932
680.0987
690.643
70.224
700.00244
710.24
720.217
730.0504
740.222
750.111
760.68
770.141
780.159
790.108
80.29
800.0831
810.379
820.0246
830.682
840.437
850.0311
860.33
870.329
880.679
890.15
90.277
900.529
910.432
920.0813
930.661
940.487
950.286
960.319
970.508
980.234
990.623



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: CNhs11016


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)
0000922 (embryo)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000295 (mouse embryonic day 12 sample)
0011316 (mouse eyeball- embryo E12 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:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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