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|library_id=CNhs11136
|library_id=CNhs11136
|library_id_phase_based=1:CNhs11136
|name=pancreas, neonate N16
|name=pancreas, neonate N16
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:14, 18 June 2014


Name:pancreas, neonate N16
Species:Mouse (Mus musculus)
Library ID:CNhs11136
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepancreas
dev stage16 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  DRS008926
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11136 CAGE DRX009063 DRR009937
Accession ID Mm9

Library idBAMCTSS
CNhs11136 DRZ001362 DRZ002745
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

CNhs11136

00
10
100
1000
10000.177
10010.0443
10020.00856
10030.0202
10040
10050
10060.147
10070.0365
10080
10090.0227
1010.103
10100.213
1011-0.108
10120.0687
10130.586
10140.114
1015-0.119
1016-0.202
10170
10180
10190
1020
10200
10210
10220.767
10230
10240.0294
10250.39
10260
1027-0.048
10280
10290.0704
1030.0474
10300.119
1031-0.0891
1032-0.00405
10330
10340.956
10350
10360.12
10370
1038-0.00865
10390.203
1040
1040-0.0399
10410.213



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: CNhs11136

Jaspar motifP-value
MA0002.20.742
MA0003.10.741
MA0004.10.175
MA0006.10.121
MA0007.10.375
MA0009.10.34
MA0014.10.608
MA0017.10.58
MA0018.24.63207e-4
MA0019.10.972
MA0024.10.0325
MA0025.10.633
MA0027.10.978
MA0028.10.903
MA0029.10.655
MA0030.10.375
MA0031.10.964
MA0035.20.27
MA0038.10.796
MA0039.20.325
MA0040.10.697
MA0041.10.365
MA0042.10.704
MA0043.10.00241
MA0046.15.13428e-10
MA0047.23.51619e-4
MA0048.10.837
MA0050.10.43
MA0051.10.677
MA0052.14.95524e-4
MA0055.10.281
MA0057.10.249
MA0058.10.374
MA0059.10.00188
MA0060.10.0936
MA0061.10.635
MA0062.20.92
MA0065.20.191
MA0066.10.868
MA0067.10.0798
MA0068.10.962
MA0069.10.356
MA0070.10.632
MA0071.10.627
MA0072.10.39
MA0073.10.996
MA0074.10.307
MA0076.10.593
MA0077.10.225
MA0078.10.517
MA0079.20.844
MA0080.20.966
MA0081.10.397
MA0083.10.741
MA0084.10.721
MA0087.10.695
MA0088.10.0314
MA0090.10.0809
MA0091.14.01067e-4
MA0092.10.17
MA0093.10.191
MA0099.20.00632
MA0100.10.0056
MA0101.10.921
MA0102.20.157
MA0103.11.351e-5
MA0104.20.117
MA0105.10.831
MA0106.10.042
MA0107.10.678
MA0108.20.0117
MA0111.10.654
MA0112.21.17243e-4
MA0113.10.708
MA0114.10.779
MA0115.10.995
MA0116.10.895
MA0117.10.539
MA0119.10.67
MA0122.10.324
MA0124.10.2
MA0125.10.222
MA0131.10.923
MA0135.10.687
MA0136.10.255
MA0137.20.00611
MA0138.20.282
MA0139.10.0846
MA0140.10.4
MA0141.10.314
MA0142.10.569
MA0143.10.29
MA0144.10.0577
MA0145.10.0817
MA0146.10.367
MA0147.10.0232
MA0148.12.17951e-5
MA0149.10.0417
MA0150.10.723
MA0152.10.521
MA0153.10.0102
MA0154.10.0118
MA0155.10.336
MA0156.10.574
MA0157.10.32
MA0159.10.577
MA0160.10.836
MA0162.10.444
MA0163.10.0666
MA0164.10.418
MA0258.10.0525
MA0259.10.497



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: CNhs11136

Novel motifP-value
10.0481
100.342
1000.683
1010.777
1020.76
1030.0649
1040.513
1050.826
1060.0176
1070.352
1080.638
1090.0462
110.256
1100.0365
1110.11
1120.0915
1130.174
1140.807
1150.915
1160.539
1170.286
1180.219
1190.101
120.386
1200.891
1210.252
1220.197
1230.424
1240.764
1250.522
1260.126
1270.62
1280.0659
1290.348
130.00407
1300.219
1310.607
1320.743
1330.0876
1340.172
1350.969
1360.786
1370.175
1380.0269
1390.488
140.759
1400.0568
1410.354
1420.777
1430.923
1440.225
1450.0253
1460.315
1470.364
1480.0847
1490.315
150.609
1500.385
1510.322
1520.0106
1530.69
1540.169
1550.454
1560.0167
1570.144
1580.11
1590.0092
1600.152
1610.392
1620.855
1630.775
1640.276
1650.236
1660.549
1670.411
1680.53
1690.0116
170.053
180.671
190.0209
20.527
200.716
210.491
220.403
230.598
240.0706
250.936
260.00386
270.604
280.773
290.322
30.396
300.788
310.417
320.55
330.98
340.678
350.45
360.485
370.031
380.527
390.228
40.274
400.827
410.139
420.182
430.286
440.817
450.824
460.108
470.772
480.329
490.117
50.525
500.504
510.628
520.441
530.66
540.793
550.543
560.376
570.627
580.17
590.215
60.819
600.184
610.111
620.295
630.0756
640.58
650.292
660.455
670.665
680.549
690.496
70.07
700.298
710.00331
720.378
730.07
740.534
750.296
760.938
770.16
780.335
790.0937
80.155
800.897
810.488
820.138
830.285
840.0276
850.0438
860.213
870.852
880.711
890.744
90.538
900.312
910.671
920.248
930.913
940.2
950.732
960.516
970.00954
980.901
990.352



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: CNhs11136


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)
0001264 (pancreas)
0002100 (trunk)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000306 (mouse neonate N16 sample)
0011267 (mouse pancreas- neonate N16 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
FF:0000294 (mouse embryonic day 11 sample)

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