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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004746
|DRA_sample_Accession=CAGE@SAMD00004746
|accession_numbers=CAGE;DRX009016;DRR009890;DRZ001315;DRZ002698
|accession_numbers=CAGE;DRX009016;DRR009890;DRZ001315;DRZ002698;DRZ012665;DRZ014048
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002107,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002107,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:29, 10 August 2017


Name:liver, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs10524
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage13 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  SAMD00004746
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10524 CAGE DRX009016 DRR009890
Accession ID Mm9

Library idBAMCTSS
CNhs10524 DRZ001315 DRZ002698
Accession ID Mm10

Library idBAMCTSS
CNhs10524 DRZ012665 DRZ014048
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

CNhs10524

00
10
100
1000
10000
1001-3.848171e-4
10020.043
1003-0.107
10040
10050
1006-0.0932
1007-0.0174
10080
1009-0.19
1010.235
10100
1011-0.108
10120
1013-0.0359
10140.114
1015-0.0209
1016-0.108
10170
10180
10190
1020
10200
10210.0779
10220
10230
10240.00443
10250.14
10260
1027-0.048
10280
1029-0.0697
103-0.0108
10300
1031-0.0914
1032-0.189
10330
10340.0779
10350
10360.314
10370
1038-0.199
1039-0.155
1040
1040-0.138
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: CNhs10524

Jaspar motifP-value
MA0002.20.245
MA0003.10.722
MA0004.10.0739
MA0006.10.697
MA0007.10.638
MA0009.10.0747
MA0014.10.851
MA0017.12.54864e-9
MA0018.20.00368
MA0019.10.263
MA0024.11.21152e-13
MA0025.10.206
MA0027.10.711
MA0028.11.38137e-5
MA0029.10.00514
MA0030.10.743
MA0031.10.767
MA0035.21.76882e-36
MA0038.10.197
MA0039.20.158
MA0040.10.195
MA0041.10.107
MA0042.10.58
MA0043.10.0793
MA0046.16.29204e-26
MA0047.20.0322
MA0048.10.0123
MA0050.10.0294
MA0051.10.0136
MA0052.17.48819e-7
MA0055.10.00179
MA0057.10.847
MA0058.10.0345
MA0059.10.00199
MA0060.15.84429e-11
MA0061.10.297
MA0062.21.59903e-6
MA0065.22.76216e-4
MA0066.10.108
MA0067.10.229
MA0068.10.381
MA0069.10.0273
MA0070.10.939
MA0071.10.494
MA0072.10.271
MA0073.10.953
MA0074.10.944
MA0076.11.8574e-4
MA0077.10.662
MA0078.10.676
MA0079.20.0721
MA0080.20.0154
MA0081.10.239
MA0083.10.265
MA0084.10.169
MA0087.10.0301
MA0088.10.017
MA0090.10.191
MA0091.10.176
MA0092.10.893
MA0093.10.0708
MA0099.20.833
MA0100.10.0381
MA0101.10.48
MA0102.20.871
MA0103.10.164
MA0104.20.0316
MA0105.10.00259
MA0106.10.995
MA0107.10.78
MA0108.20.279
MA0111.10.673
MA0112.20.107
MA0113.10.256
MA0114.11.373e-7
MA0115.13.10902e-4
MA0116.10.0017
MA0117.10.966
MA0119.10.225
MA0122.10.822
MA0124.10.772
MA0125.10.569
MA0131.10.213
MA0135.10.43
MA0136.10.00374
MA0137.20.555
MA0138.20.00388
MA0139.10.242
MA0140.12.995e-75
MA0141.10.344
MA0142.10.0668
MA0143.10.3
MA0144.10.682
MA0145.10.555
MA0146.10.0764
MA0147.10.0128
MA0148.10.00278
MA0149.10.0579
MA0150.17.68936e-4
MA0152.10.499
MA0153.11.52462e-20
MA0154.10.141
MA0155.10.675
MA0156.16.49087e-4
MA0157.10.333
MA0159.10.0921
MA0160.10.184
MA0162.10.295
MA0163.11.15471e-6
MA0164.10.237
MA0258.10.892
MA0259.10.213



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: CNhs10524

Novel motifP-value
10.255
100.0819
1000.147
1010.427
1020.504
1030.0431
1040.712
1050.914
1060.878
1070.919
1080.531
1090.016
110.222
1100.0985
1110.00649
1120.0466
1130.513
1140.76
1150.91
1160.718
1170.00203
1180.0276
1190.812
120.947
1200.982
1210.173
1220.573
1230.0226
1240.0742
1250.745
1260.0473
1270.346
1280.588
1290.867
136.79977e-6
1300.394
1310.332
1320.0268
1330.299
1340.0704
1350.463
1360.23
1370.31
1380.821
1390.678
140.627
1400.772
1410.0558
1420.0805
1430.829
1440.819
1450.00481
1460.706
1470.749
1480.156
1490.199
150.0718
1500.222
1510.701
1520.941
1530.855
1540.466
1550.61
1560.0279
1570.974
1580.282
1590.562
1600.506
1610.00566
1620.583
1630.638
1643.34774e-4
1650.5
1660.209
1670.182
1680.603
1690.0833
170.922
180.439
190.343
20.344
200.00846
210.727
220.705
230.228
240.477
250.436
266.90933e-4
270.929
280.735
290.00227
30.0452
300.893
310.867
320.853
330.143
340.653
350.553
360.017
370.301
380.731
390.909
40.378
400.101
410.665
420.0499
430.2
440.889
450.822
460.121
470.128
480.18
490.0988
50.196
500.739
510.917
520.853
530.827
540.948
550.172
560.924
570.467
580.826
590.587
60.897
600.529
610.62
620.214
630.687
640.598
650.862
660.148
670.193
680.761
690.439
70.0181
700.542
710.00432
720.632
730.372
740.441
750.0787
760.381
770.424
780.0163
790.542
80.00453
800.108
810.888
820.824
830.539
840.653
850.591
860.379
870.0369
880.682
890.957
90.74
900.251
910.838
920.983
930.795
940.244
950.0557
960.219
970.563
980.363
990.915



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: CNhs10524


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)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011328 (mouse liver- embryo E13 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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