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|library_id=CNhs11106
|library_id=CNhs11106
|library_id_phase_based=1:CNhs11106
|name=liver, neonate N30
|name=liver, neonate N30
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:10, 18 June 2014


Name:liver, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11106
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
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  DRS008892
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11106 CAGE DRX009029 DRR009903
Accession ID Mm9

Library idBAMCTSS
CNhs11106 DRZ001328 DRZ002711
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

CNhs11106

00
10
100
1000
10000
10010.202
1002-0.0941
10030.0147
10040
10050
10060
1007-0.0267
10080
10090.0336
101-0.0331
10100
1011-0.298
10120
10130.536
10140
1015-0.266
1016-0.423
10170
10180
10190
1020
10200
10210
10220.646
10230
10240.0811
10250.389
10260
10270
10280
1029-0.005
103-0.0659
10300
1031-0.0495
1032-0.4
1033-0.0665
10341.033
10350
1036-0.324
10370
1038-0.17
10390.892
1040
1040-0.216
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: CNhs11106

Jaspar motifP-value
MA0002.20.587
MA0003.10.672
MA0004.10.455
MA0006.10.216
MA0007.10.0981
MA0009.10.452
MA0014.10.165
MA0017.19.97493e-24
MA0018.24.48636e-4
MA0019.10.481
MA0024.12.56906e-4
MA0025.10.121
MA0027.10.809
MA0028.10.569
MA0029.10.333
MA0030.13.00124e-4
MA0031.13.00358e-4
MA0035.20.192
MA0038.10.682
MA0039.20.425
MA0040.10.205
MA0041.10.809
MA0042.10.988
MA0043.10.151
MA0046.11.24382e-79
MA0047.25.42224e-9
MA0048.10.28
MA0050.10.021
MA0051.10.0152
MA0052.10.00572
MA0055.10.305
MA0057.10.612
MA0058.10.285
MA0059.10.0989
MA0060.10.00427
MA0061.10.517
MA0062.20.74
MA0065.22.25501e-17
MA0066.10.0239
MA0067.10.297
MA0068.10.423
MA0069.10.407
MA0070.10.442
MA0071.14.45847e-6
MA0072.12.3437e-6
MA0073.10.687
MA0074.10.0874
MA0076.10.944
MA0077.10.0537
MA0078.10.757
MA0079.20.456
MA0080.20.402
MA0081.10.552
MA0083.10.00164
MA0084.10.651
MA0087.10.421
MA0088.10.369
MA0090.10.677
MA0091.10.917
MA0092.10.0976
MA0093.10.471
MA0099.20.467
MA0100.10.569
MA0101.10.919
MA0102.20.179
MA0103.10.166
MA0104.20.94
MA0105.10.145
MA0106.10.062
MA0107.10.767
MA0108.23.05594e-4
MA0111.10.867
MA0112.27.07994e-6
MA0113.10.247
MA0114.13.75978e-23
MA0115.14.25869e-11
MA0116.10.188
MA0117.10.526
MA0119.10.0346
MA0122.10.219
MA0124.10.488
MA0125.10.498
MA0131.10.939
MA0135.10.464
MA0136.10.177
MA0137.20.081
MA0138.20.436
MA0139.10.377
MA0140.10.643
MA0141.11.78798e-8
MA0142.10.111
MA0143.10.429
MA0144.10.199
MA0145.10.138
MA0146.10.0307
MA0147.10.957
MA0148.17.11055e-12
MA0149.10.00753
MA0150.10.00681
MA0152.10.564
MA0153.13.10829e-56
MA0154.10.158
MA0155.10.559
MA0156.10.677
MA0157.13.4051e-4
MA0159.14.13464e-4
MA0160.15.80247e-6
MA0162.10.528
MA0163.10.00509
MA0164.10.724
MA0258.10.00506
MA0259.10.656



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: CNhs11106

Novel motifP-value
10.106
100.206
1000.596
1010.665
1020.241
1030.0106
1040.776
1050.821
1060.0542
1070.0922
1080.531
1090.0618
110.0642
1100.0592
1110.0249
1120.00273
1130.971
1140.0118
1150.274
1160.653
1170.0543
1180.209
1190.0586
120.358
1200.548
1210.691
1220.288
1230.193
1240.504
1250.316
1260.222
1270.817
1280.0466
1290.816
137.69856e-5
1300.852
1310.383
1320.348
1330.683
1340.943
1350.504
1360.229
1370.897
1380.347
1390.74
140.462
1400.00928
1410.366
1420.105
1430.793
1440.475
1450.0378
1460.323
1470.474
1480.335
1490.319
150.17
1500.164
1510.52
1520.121
1530.241
1540.716
1550.546
1560.0418
1570.697
1580.654
1590.494
1600.186
1610.657
1620.611
1630.166
1640.0338
1650.42
1660.366
1670.216
1680.848
1690.00331
170.065
180.907
190.0416
20.722
200.312
210.471
220.114
230.435
240.149
250.744
260.00326
270.916
280.392
290.28
30.0754
300.928
310.394
320.127
330.344
340.937
350.504
360.0584
370.0359
380.307
390.182
40.686
400.134
410.954
420.492
430.0821
440.0492
450.68
460.126
470.691
480.18
490.0447
50.122
500.585
510.277
520.391
530.535
540.339
550.744
560.452
570.788
580.275
590.245
60.756
600.103
610.196
620.106
630.0868
640.55
650.222
660.594
670.949
680.149
690.878
70.186
700.0216
710.0538
720.725
730.058
740.636
750.0155
760.894
770.451
780.0173
790.946
80.0128
800.75
810.639
820.0255
830.434
840.289
850.0304
860.146
870.21
880.76
890.166
90.881
900.0652
910.334
920.292
930.195
940.731
950.215
960.199
970.523
980.417
990.0914



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: CNhs11106


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

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)
0011486 (mouse liver- 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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