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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008943
|DRA_sample_Accession=CAGE@SAMD00005816
|accession_numbers=CAGE;DRX009080;DRR009954;DRZ001379;DRZ002762
|accession_numbers=CAGE;DRX009080;DRR009954;DRZ001379;DRZ002762
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000014,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0007029,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000014,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0007029,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416

Revision as of 21:59, 31 July 2014


Name:skin, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11097
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueskin
dev stage6 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  SAMD00005816
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11097 CAGE DRX009080 DRR009954
Accession ID Mm9

Library idBAMCTSS
CNhs11097 DRZ001379 DRZ002762
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

CNhs11097

00
10
100
1000
10000.0922
10010
10020.049
10030.148
10040
10050
1006-0.033
10070.0725
10080
10090.219
1010.0515
10100
1011-0.0324
10120
1013-0.0663
10140.00563
1015-0.0612
1016-0.0346
10170
10180.626
10190
1020
10200
10210
10220.0728
10230
10240.133
1025-0.0122
10260
10270
10280
10290.0586
1030.507
10300
10310.128
1032-0.0533
1033-0.0262
10340.049
10350
1036-0.00147
10370
1038-0.00712
1039-0.131
1040
10400.126
10410.498



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: CNhs11097

Jaspar motifP-value
MA0002.20.931
MA0003.10.481
MA0004.10.805
MA0006.10.0517
MA0007.10.683
MA0009.10.0311
MA0014.10.295
MA0017.12.49169e-6
MA0018.20.0266
MA0019.10.0588
MA0024.10.54
MA0025.10.677
MA0027.10.884
MA0028.11.93207e-4
MA0029.10.429
MA0030.10.411
MA0031.10.523
MA0035.20.00147
MA0038.10.248
MA0039.27.87253e-4
MA0040.10.0264
MA0041.10.188
MA0042.10.715
MA0043.10.298
MA0046.16.54956e-18
MA0047.20.194
MA0048.10.121
MA0050.10.0076
MA0051.10.0658
MA0052.10.00542
MA0055.19.46352e-4
MA0057.10.117
MA0058.10.51
MA0059.10.394
MA0060.10.89
MA0061.10.144
MA0062.25.4432e-7
MA0065.20.107
MA0066.10.465
MA0067.10.752
MA0068.10.484
MA0069.10.867
MA0070.10.753
MA0071.10.0578
MA0072.10.962
MA0073.10.607
MA0074.10.19
MA0076.12.7022e-4
MA0077.10.576
MA0078.10.123
MA0079.20.0317
MA0080.22.22316e-6
MA0081.10.00136
MA0083.10.113
MA0084.10.631
MA0087.10.707
MA0088.10.666
MA0090.10.00444
MA0091.10.555
MA0092.10.0801
MA0093.10.706
MA0099.23.33529e-15
MA0100.10.0629
MA0101.10.365
MA0102.20.225
MA0103.10.00177
MA0104.20.153
MA0105.10.207
MA0106.10.0136
MA0107.10.43
MA0108.24.63043e-51
MA0111.10.96
MA0112.20.612
MA0113.10.0173
MA0114.11.87416e-5
MA0115.11.78274e-4
MA0116.10.646
MA0117.10.513
MA0119.10.593
MA0122.10.522
MA0124.10.523
MA0125.16.38918e-5
MA0131.10.482
MA0135.10.0675
MA0136.11.07484e-6
MA0137.20.254
MA0138.20.827
MA0139.10.364
MA0140.10.00105
MA0141.11.7393e-4
MA0142.10.542
MA0143.10.316
MA0144.10.786
MA0145.10.0525
MA0146.10.275
MA0147.10.0982
MA0148.10.235
MA0149.10.308
MA0150.10.833
MA0152.10.533
MA0153.13.63679e-12
MA0154.10.467
MA0155.10.794
MA0156.13.88507e-6
MA0157.10.0485
MA0159.10.0538
MA0160.10.00384
MA0162.10.568
MA0163.10.551
MA0164.10.226
MA0258.10.396
MA0259.10.254



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: CNhs11097

Novel motifP-value
10.846
100.964
1000.681
1010.653
1020.286
1030.443
1040.0494
1050.539
1060.0181
1070.0222
1080.511
1090.97
110.97
1100.919
1110.485
1120.659
1130.916
1140.641
1150.268
1160.719
1170.55
1180.102
1190.835
120.792
1200.924
1210.733
1220.864
1230.991
1240.357
1250.872
1260.688
1270.969
1280.0716
1290.89
130.0285
1300.578
1310.21
1320.963
1330.432
1340.673
1350.108
1360.137
1370.473
1380.156
1390.322
140.43
1400.125
1410.846
1420.452
1430.574
1440.615
1450.205
1460.649
1470.133
1480.243
1490.476
150.101
1500.237
1510.711
1520.0114
1530.733
1540.478
1550.968
1563.76453e-4
1570.0391
1580.223
1590.0327
1600.236
1610.356
1620.846
1630.737
1640.574
1650.347
1660.369
1670.0159
1680.533
1690.0549
170.0404
180.306
190.333
20.0419
200.117
210.412
220.463
230.0627
240.723
250.253
260.00238
270.842
280.948
290.353
30.793
300.0273
310.279
320.701
330.896
340.769
350.0186
360.0437
370.576
380.997
390.0347
40.916
400.596
410.71
420.653
430.935
440.444
450.357
460.521
470.858
480.95
490.409
50.341
500.603
510.861
520.0661
530.214
540.536
550.279
560.889
570.47
580.888
590.378
60.478
600.0602
610.513
620.776
630.591
640.501
650.782
660.671
670.6
680.045
690.0618
70.507
700.435
710.513
720.775
730.101
740.823
750.509
760.00315
770.0594
780.0152
790.826
80.46
800.17
810.432
820.837
830.379
840.674
850.0797
860.127
870.0333
880.735
890.368
90.403
900.857
910.799
920.781
930.548
940.369
950.351
960.819
970.0655
980.881
990.107



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: CNhs11097


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)
0000014 (zone of skin)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0007029 (surface)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011406 (mouse skin- neonate N06 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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