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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008888
|DRA_sample_Accession=CAGE@SAMD00005798
|accession_numbers=CAGE;DRX009025;DRR009899;DRZ001324;DRZ002707
|accession_numbers=CAGE;DRX009025;DRR009899;DRZ001324;DRZ002707
|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

Revision as of 22:00, 31 July 2014


Name:liver, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11103
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage7 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  SAMD00005798
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11103 CAGE DRX009025 DRR009899
Accession ID Mm9

Library idBAMCTSS
CNhs11103 DRZ001324 DRZ002707
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

CNhs11103

00
10
100
1000
10000
10010.175
1002-0.0612
1003-0.0892
10040
10050.203
10060.00427
10070.00843
10080
10090.022
101-0.0174
10100
1011-0.16
10120.137
10130.334
10140.122
1015-0.263
1016-0.223
10170
10180
10190
1020
10200
10210
10220.393
10230
10240.137
10250.638
10260
10270
10280
1029-0.0818
1030
10300
1031-0.00421
1032-0.232
10330
10340.51
10350
1036-0.054
10370
1038-0.0389
10390.446
1040
1040-0.0865
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: CNhs11103

Jaspar motifP-value
MA0002.20.0402
MA0003.10.248
MA0004.10.95
MA0006.10.152
MA0007.10.637
MA0009.10.497
MA0014.10.539
MA0017.11.85065e-19
MA0018.21.65906e-6
MA0019.10.2
MA0024.10.168
MA0025.10.344
MA0027.10.889
MA0028.10.355
MA0029.10.149
MA0030.10.0024
MA0031.10.0102
MA0035.20.0192
MA0038.10.737
MA0039.20.378
MA0040.10.145
MA0041.10.504
MA0042.10.823
MA0043.10.0406
MA0046.15.18929e-75
MA0047.22.76294e-9
MA0048.10.366
MA0050.12.86326e-6
MA0051.13.17172e-5
MA0052.10.0166
MA0055.10.821
MA0057.10.84
MA0058.10.832
MA0059.10.483
MA0060.10.00728
MA0061.10.182
MA0062.20.166
MA0065.22.87921e-13
MA0066.10.0252
MA0067.10.0694
MA0068.10.606
MA0069.10.287
MA0070.10.419
MA0071.19.17655e-4
MA0072.10.00247
MA0073.10.757
MA0074.10.284
MA0076.10.109
MA0077.10.0211
MA0078.10.46
MA0079.20.5
MA0080.20.013
MA0081.10.73
MA0083.10.135
MA0084.10.432
MA0087.10.106
MA0088.10.664
MA0090.10.703
MA0091.10.916
MA0092.10.0518
MA0093.10.962
MA0099.20.383
MA0100.10.345
MA0101.10.663
MA0102.20.183
MA0103.10.403
MA0104.20.461
MA0105.10.0082
MA0106.10.0706
MA0107.10.626
MA0108.20.0166
MA0111.10.876
MA0112.21.48684e-5
MA0113.10.497
MA0114.16.06614e-19
MA0115.14.02358e-11
MA0116.10.0302
MA0117.10.808
MA0119.10.00177
MA0122.10.507
MA0124.10.661
MA0125.10.71
MA0131.10.693
MA0135.10.703
MA0136.10.736
MA0137.20.372
MA0138.20.815
MA0139.10.107
MA0140.10.00424
MA0141.13.99008e-4
MA0142.10.199
MA0143.10.11
MA0144.10.376
MA0145.10.116
MA0146.10.132
MA0147.10.518
MA0148.14.96153e-13
MA0149.10.162
MA0150.10.114
MA0152.10.413
MA0153.18.05743e-50
MA0154.10.019
MA0155.10.306
MA0156.10.779
MA0157.10.00349
MA0159.10.00252
MA0160.10.00175
MA0162.10.446
MA0163.19.34499e-5
MA0164.10.916
MA0258.10.0116
MA0259.10.329



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: CNhs11103

Novel motifP-value
10.185
100.226
1000.759
1010.899
1020.0879
1030.00696
1040.479
1050.932
1060.0118
1070.0158
1080.71
1090.0682
110.142
1100.0816
1110.152
1120.00663
1130.894
1140.0678
1150.455
1160.911
1170.125
1180.186
1190.148
120.55
1200.604
1210.456
1220.818
1230.23
1240.133
1250.455
1260.227
1270.83
1280.0104
1290.712
132.32836e-4
1300.287
1310.0486
1320.604
1330.369
1340.873
1350.363
1360.433
1370.451
1380.354
1390.97
140.475
1400.0784
1410.662
1420.182
1430.63
1440.947
1450.0298
1460.23
1470.479
1480.771
1490.314
150.137
1500.141
1510.467
1520.113
1530.127
1540.691
1550.537
1560.201
1570.426
1580.215
1590.391
1600.0617
1610.964
1620.411
1630.983
1640.0733
1650.548
1660.264
1670.456
1680.591
1690.00171
170.08
180.893
190.0201
20.425
200.714
210.47
220.106
230.202
240.261
250.996
268.62157e-4
270.504
280.511
290.42
30.0313
300.656
310.334
320.0493
330.176
340.699
350.914
360.0575
370.0877
380.322
390.241
40.681
400.132
410.612
420.177
430.056
440.143
450.589
460.0974
470.369
480.215
490.0686
50.101
500.406
510.251
520.125
530.917
540.386
550.517
560.354
570.989
580.364
590.0628
60.956
600.0764
610.221
620.164
630.0778
640.526
650.23
660.659
670.994
680.222
690.657
70.157
700.2
710.0634
720.633
730.187
740.396
750.0758
760.748
770.305
780.0172
790.89
80.0331
800.148
810.717
820.0884
830.721
840.862
850.0594
860.204
870.286
880.895
890.046
90.475
900.309
910.2
920.237
930.452
940.803
950.274
960.227
970.826
980.244
990.0424



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: CNhs11103


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)
0000313 (mouse neonate N7 sample)
0011409 (mouse liver- neonate N07 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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