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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008880
|DRA_sample_Accession=CAGE@SAMD00005338
|accession_numbers=CAGE;DRX009017;DRR009891;DRZ001316;DRZ002699
|accession_numbers=CAGE;DRX009017;DRR009891;DRZ001316;DRZ002699
|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

Revision as of 21:51, 31 July 2014


Name:liver, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10594
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage14 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  SAMD00005338
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10594 CAGE DRX009017 DRR009891
Accession ID Mm9

Library idBAMCTSS
CNhs10594 DRZ001316 DRZ002699
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

CNhs10594

00
10
100
1000
1000-0.0355
10010
1002-0.00274
1003-0.112
10040
10050
1006-0.143
10074.236979e-4
10080
1009-0.172
1010.208
10100
1011-0.108
10120
1013-0.176
10140.0683
1015-0.0558
1016-0.291
10170
10180
10190
1020
10200
10210.0881
1022-0.186
10230
1024-0.00178
10250.253
10260
1027-0.048
10280
10290.0471
103-0.0595
10300
1031-0.184
1032-0.333
10330.0129
10340
10350
10360.358
10370
1038-0.342
1039-0.0945
1040
1040-0.211
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: CNhs10594

Jaspar motifP-value
MA0002.20.042
MA0003.10.999
MA0004.10.234
MA0006.10.634
MA0007.10.408
MA0009.10.084
MA0014.10.891
MA0017.11.57093e-8
MA0018.20.0073
MA0019.10.294
MA0024.11.03426e-8
MA0025.10.344
MA0027.10.839
MA0028.16.06458e-4
MA0029.10.0477
MA0030.10.907
MA0031.10.682
MA0035.21.2573e-25
MA0038.10.169
MA0039.20.351
MA0040.10.431
MA0041.10.367
MA0042.10.547
MA0043.10.0762
MA0046.16.92154e-25
MA0047.20.0406
MA0048.10.0253
MA0050.10.542
MA0051.10.38
MA0052.17.61991e-7
MA0055.10.00887
MA0057.10.666
MA0058.10.176
MA0059.10.00959
MA0060.12.12546e-4
MA0061.10.204
MA0062.24.98778e-5
MA0065.27.48039e-5
MA0066.10.0272
MA0067.10.357
MA0068.10.0203
MA0069.10.0526
MA0070.10.655
MA0071.10.175
MA0072.10.106
MA0073.10.766
MA0074.10.735
MA0076.10.00326
MA0077.10.258
MA0078.10.813
MA0079.20.0558
MA0080.20.002
MA0081.10.572
MA0083.10.0263
MA0084.10.0569
MA0087.10.0333
MA0088.10.0211
MA0090.10.287
MA0091.10.281
MA0092.10.6
MA0093.10.233
MA0099.20.973
MA0100.10.024
MA0101.10.399
MA0102.20.695
MA0103.10.783
MA0104.20.121
MA0105.18.80262e-4
MA0106.10.458
MA0107.10.955
MA0108.20.012
MA0111.10.97
MA0112.20.00734
MA0113.10.161
MA0114.16.22236e-8
MA0115.11.49902e-5
MA0116.16.49299e-4
MA0117.10.861
MA0119.10.165
MA0122.10.241
MA0124.10.875
MA0125.10.676
MA0131.10.43
MA0135.10.395
MA0136.10.00107
MA0137.20.402
MA0138.20.0179
MA0139.10.165
MA0140.13.16649e-59
MA0141.10.0419
MA0142.10.0759
MA0143.10.365
MA0144.10.676
MA0145.10.712
MA0146.10.11
MA0147.10.0711
MA0148.13.27097e-4
MA0149.10.0293
MA0150.10.0011
MA0152.10.747
MA0153.12.77384e-22
MA0154.10.0673
MA0155.10.692
MA0156.10.00128
MA0157.10.442
MA0159.10.0625
MA0160.10.0393
MA0162.10.237
MA0163.11.59989e-6
MA0164.10.218
MA0258.10.219
MA0259.10.274



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: CNhs10594

Novel motifP-value
10.103
100.0411
1000.211
1010.623
1020.858
1030.016
1040.901
1050.813
1060.667
1070.858
1080.372
1090.011
110.103
1100.0458
1110.00491
1120.0279
1130.628
1140.39
1150.518
1160.878
1170.00153
1180.0291
1190.346
120.943
1200.995
1210.334
1220.91
1230.0469
1240.268
1250.36
1260.104
1270.204
1280.625
1290.586
131.03034e-4
1300.563
1310.606
1320.0883
1330.254
1340.249
1350.215
1360.512
1370.277
1380.896
1390.714
140.839
1400.328
1410.274
1420.128
1430.883
1440.797
1450.00775
1460.581
1470.906
1480.316
1490.634
150.0364
1500.246
1510.546
1520.885
1530.792
1540.963
1550.196
1563.71578e-7
1570.722
1580.078
1590.315
1600.38
1610.0317
1620.837
1630.937
1640.00155
1650.702
1660.249
1670.0718
1680.602
1690.0287
170.547
180.292
190.291
20.337
200.0244
210.814
220.525
230.397
240.479
250.389
267.86077e-4
270.974
280.411
290.0031
30.025
300.734
310.939
320.812
330.14
340.95
350.944
360.0222
370.184
380.835
390.682
40.677
400.108
410.665
420.0565
430.119
440.965
450.783
460.103
470.167
480.169
490.0663
50.041
500.873
510.591
520.914
530.767
540.746
550.319
560.727
570.345
580.498
590.557
60.88
600.467
610.297
620.127
630.48
640.369
650.818
660.338
670.4
680.724
690.748
70.0445
700.552
710.00619
720.439
730.31
740.499
750.0296
760.36
770.857
780.00883
790.435
80.00718
800.0909
810.874
820.832
830.645
840.971
850.648
860.465
870.59
880.696
890.8
90.992
900.0678
910.335
920.617
930.679
940.207
950.0359
960.116
970.567
980.214
990.776



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: CNhs10594


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)
0000296 (mouse embryonic day 14 sample)
0011340 (mouse liver- embryo E14 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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