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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004760
|DRA_sample_Accession=CAGE@SAMD00004760
|accession_numbers=CAGE;DRX009028;DRR009902;DRZ001327;DRZ002710
|accession_numbers=CAGE;DRX009028;DRR009902;DRZ001327;DRZ002710;DRZ012677;DRZ014060
|ancestors_in_anatomy_facet=UBERON:0000468,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: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 22:15, 10 August 2017


Name:liver, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11198
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage25 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  SAMD00004760
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11198 CAGE DRX009028 DRR009902
Accession ID Mm9

Library idBAMCTSS
CNhs11198 DRZ001327 DRZ002710
Accession ID Mm10

Library idBAMCTSS
CNhs11198 DRZ012677 DRZ014060
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

CNhs11198

00
10
100
1000
10000.162
10010.116
1002-0.116
10030.0278
10040
10050.00294
10060.107
1007-0.0939
10080
10090.0434
1010.00851
10100
1011-0.182
10120
10130.496
1014-0.0874
1015-0.37
1016-0.362
10170
10180
10190
1020
10200
10210.116
10220.523
10230
10240
10250.235
10260
10270
10280
1029-0.0428
103-0.0563
10300
1031-0.217
1032-0.268
10330
10340.862
10350
1036-0.208
10370
1038-0.191
10390.718
1040
1040-0.141
10410.0717



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: CNhs11198

Jaspar motifP-value
MA0002.20.316
MA0003.10.517
MA0004.10.657
MA0006.10.236
MA0007.10.268
MA0009.10.629
MA0014.10.263
MA0017.13.06405e-24
MA0018.27.55013e-5
MA0019.10.572
MA0024.10.0625
MA0025.10.181
MA0027.10.687
MA0028.10.429
MA0029.10.483
MA0030.10.0144
MA0031.10.00237
MA0035.20.0432
MA0038.10.324
MA0039.20.248
MA0040.10.589
MA0041.10.826
MA0042.10.997
MA0043.10.23
MA0046.11.42394e-103
MA0047.22.78536e-8
MA0048.10.341
MA0050.10.00401
MA0051.10.00288
MA0052.10.97
MA0055.10.213
MA0057.10.531
MA0058.10.441
MA0059.10.135
MA0060.10.889
MA0061.10.527
MA0062.20.842
MA0065.21.71533e-16
MA0066.10.0397
MA0067.10.0905
MA0068.10.287
MA0069.10.0737
MA0070.10.2
MA0071.12.32266e-5
MA0072.11.85889e-6
MA0073.10.907
MA0074.10.306
MA0076.10.967
MA0077.10.0275
MA0078.10.586
MA0079.20.281
MA0080.20.332
MA0081.10.536
MA0083.10.0841
MA0084.10.444
MA0087.10.255
MA0088.10.203
MA0090.10.436
MA0091.10.844
MA0092.10.196
MA0093.10.665
MA0099.20.559
MA0100.10.364
MA0101.10.844
MA0102.20.158
MA0103.10.181
MA0104.20.933
MA0105.10.086
MA0106.10.0333
MA0107.10.758
MA0108.20.0968
MA0111.10.697
MA0112.28.34929e-6
MA0113.10.432
MA0114.11.72291e-24
MA0115.14.96652e-12
MA0116.10.0996
MA0117.10.717
MA0119.10.00825
MA0122.10.577
MA0124.10.562
MA0125.10.612
MA0131.10.87
MA0135.10.621
MA0136.10.156
MA0137.20.0558
MA0138.20.377
MA0139.10.152
MA0140.10.546
MA0141.11.22638e-7
MA0142.10.0921
MA0143.10.213
MA0144.10.29
MA0145.10.0654
MA0146.10.153
MA0147.10.829
MA0148.16.03629e-11
MA0149.10.00896
MA0150.10.00301
MA0152.10.573
MA0153.14.45591e-68
MA0154.10.129
MA0155.10.65
MA0156.10.534
MA0157.10.00113
MA0159.12.42461e-4
MA0160.18.98409e-6
MA0162.10.314
MA0163.10.00276
MA0164.10.805
MA0258.10.00115
MA0259.10.606



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: CNhs11198

Novel motifP-value
10.0758
100.178
1000.581
1010.952
1020.125
1030.011
1040.669
1050.421
1060.132
1070.12
1080.388
1090.0515
110.0726
1100.0276
1110.0482
1120.0142
1130.965
1140.0477
1150.557
1160.894
1170.0688
1180.541
1190.0758
120.637
1200.388
1210.432
1220.351
1230.126
1240.805
1250.196
1260.302
1270.879
1280.151
1290.598
132.2796e-5
1300.875
1310.184
1320.57
1330.593
1340.56
1350.599
1360.376
1370.955
1380.406
1390.825
140.417
1400.179
1410.43
1420.197
1430.995
1440.634
1450.0615
1460.322
1470.456
1480.231
1490.301
150.178
1500.248
1510.666
1520.148
1530.251
1540.711
1550.938
1560.114
1570.471
1580.593
1590.413
1600.169
1610.718
1620.65
1630.242
1640.0645
1650.351
1660.137
1670.412
1680.691
1696.09801e-4
170.0591
180.822
190.036
20.899
200.455
210.39
220.122
230.405
240.224
250.57
260.00338
270.87
280.492
290.247
30.0612
300.86
310.363
320.239
330.224
340.844
350.483
360.0646
370.0638
380.262
390.25
40.809
400.11
410.898
420.384
430.113
440.0429
450.675
460.135
470.34
480.135
490.092
50.127
500.602
510.295
520.4
530.581
540.404
550.535
560.505
570.972
580.292
590.255
60.81
600.203
610.265
620.136
630.0955
640.52
650.196
660.926
670.844
680.443
690.945
70.14
700.0922
710.0439
720.798
730.0886
740.545
750.0264
760.682
770.423
780.00948
790.996
80.0122
800.502
810.638
820.0428
830.477
840.398
850.0349
860.163
870.144
880.768
890.0752
90.804
900.0748
910.382
920.384
930.089
940.964
950.184
960.281
970.324
980.627
990.092



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: CNhs11198


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)
0000309 (mouse neonate N25 sample)
0011485 (mouse liver- neonate N25 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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