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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008813
|DRA_sample_Accession=CAGE@SAMD00005403
|accession_numbers=CAGE;DRX008950;DRR009824;DRZ001249;DRZ002632
|accession_numbers=CAGE;DRX008950;DRR009824;DRZ001249;DRZ002632
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890

Revision as of 21:38, 31 July 2014


Name:diencephalon, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11201
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuediencephalon
dev stage30 days neonate
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  SAMD00005403
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11201 CAGE DRX008950 DRR009824
Accession ID Mm9

Library idBAMCTSS
CNhs11201 DRZ001249 DRZ002632
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

CNhs11201

00
10.756
100
1000.0653
1000-0.0106
10010.0303
1002-0.083
1003-0.0221
10040
10050.115
10060.585
10070.0346
10080
1009-0.19
101-0.0595
10100
10110.66
10120.361
10130.174
1014-0.0874
1015-0.0603
1016-0.0945
10170
10180
10190
1020
10200
10210
10220
10230
10240.118
10250
10260
10270.508
10280
10290.143
103-0.0829
10300
1031-0.356
10320.402
10330
10340
10350.0532
1036-0.244
10370
10380.0308
10390.136
1040
1040-0.31
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: CNhs11201

Jaspar motifP-value
MA0002.20.00125
MA0003.10.296
MA0004.10.485
MA0006.10.181
MA0007.10.389
MA0009.10.741
MA0014.10.641
MA0017.11.38324e-6
MA0018.20.0132
MA0019.10.346
MA0024.10.0582
MA0025.10.00457
MA0027.10.0591
MA0028.10.0706
MA0029.10.437
MA0030.10.798
MA0031.10.214
MA0035.20.0133
MA0038.10.285
MA0039.20.0383
MA0040.10.325
MA0041.10.115
MA0042.10.221
MA0043.10.0562
MA0046.11.0205e-11
MA0047.28.53604e-5
MA0048.10.0428
MA0050.11.9755e-5
MA0051.10.00199
MA0052.10.846
MA0055.10.012
MA0057.10.357
MA0058.10.43
MA0059.10.132
MA0060.10.716
MA0061.10.033
MA0062.20.00135
MA0065.21.30554e-6
MA0066.10.03
MA0067.10.562
MA0068.10.4
MA0069.10.0643
MA0070.10.83
MA0071.10.0561
MA0072.10.428
MA0073.10.774
MA0074.10.116
MA0076.10.168
MA0077.10.401
MA0078.10.793
MA0079.20.341
MA0080.23.04834e-10
MA0081.10.237
MA0083.10.00941
MA0084.10.903
MA0087.10.248
MA0088.10.243
MA0090.10.125
MA0091.10.214
MA0092.10.203
MA0093.10.534
MA0099.20.00278
MA0100.10.276
MA0101.10.0169
MA0102.20.481
MA0103.10.197
MA0104.20.83
MA0105.10.00699
MA0106.10.0527
MA0107.10.0423
MA0108.20.00286
MA0111.10.977
MA0112.27.19482e-4
MA0113.10.358
MA0114.15.98976e-6
MA0115.15.89665e-6
MA0116.10.0631
MA0117.10.955
MA0119.10.115
MA0122.10.959
MA0124.10.447
MA0125.10.0186
MA0131.10.713
MA0135.10.581
MA0136.11.41749e-12
MA0137.20.0611
MA0138.21.73492e-4
MA0139.10.493
MA0140.11.97393e-4
MA0141.10.00287
MA0142.10.236
MA0143.10.955
MA0144.10.0446
MA0145.10.145
MA0146.10.0247
MA0147.10.666
MA0148.13.75712e-4
MA0149.10.105
MA0150.10.159
MA0152.10.216
MA0153.14.05514e-11
MA0154.10.045
MA0155.10.406
MA0156.12.8707e-8
MA0157.10.105
MA0159.10.0014
MA0160.10.00444
MA0162.10.148
MA0163.17.54726e-4
MA0164.10.82
MA0258.10.0178
MA0259.10.838



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: CNhs11201

Novel motifP-value
10.202
100.0477
1000.385
1010.836
1020.955
1030.0617
1040.954
1050.666
1060.0609
1070.179
1080.709
1090.00999
110.0717
1100.0419
1110.118
1120.00602
1130.498
1140.33
1150.895
1160.197
1170.00361
1180.338
1190.213
120.949
1200.718
1210.564
1220.61
1238.15991e-4
1240.0544
1250.236
1260.0266
1270.214
1280.0573
1290.371
134.20859e-7
1300.205
1310.734
1320.668
1330.863
1340.113
1350.265
1360.039
1370.705
1380.912
1390.276
140.889
1400.0232
1410.63
1420.917
1430.362
1440.799
1452.93122e-4
1460.331
1470.359
1480.722
1490.9
150.214
1500.0601
1510.839
1520.0993
1530.85
1540.959
1550.29
1560.00655
1570.213
1580.317
1590.612
1600.178
1610.0997
1620.661
1630.657
1640.0402
1650.147
1660.814
1670.644
1680.554
1690.00337
170.0545
180.861
190.102
20.786
200.035
210.213
220.149
230.741
240.0631
250.698
269.73217e-8
270.566
280.774
290.0278
30.0613
300.767
310.929
320.468
330.136
340.738
350.807
360.215
370.0261
380.547
390.342
40.257
400.0987
410.444
420.179
430.127
440.399
450.712
460.101
470.354
480.265
490.193
50.155
500.246
510.747
520.353
530.425
540.943
550.923
560.477
570.582
580.342
590.11
60.814
600.0454
610.0463
620.223
630.174
640.642
650.407
660.699
670.63
680.798
690.493
70.0195
700.0634
710.00389
720.459
730.0355
740.896
750.0459
760.409
770.407
780.00187
790.416
80.0542
800.401
810.783
820.232
830.106
840.807
850.208
860.159
870.119
880.453
890.661
90.469
900.214
910.12
920.222
930.0722
940.813
950.0346
960.313
970.977
980.523
990.43



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: CNhs11201


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)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
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)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011470 (mouse diencephalon- neonate N30 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:0006222 (future diencephalon)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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