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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005553
|DRA_sample_Accession=CAGE@SAMD00005553
|accession_numbers=CAGE;DRX009003;DRR009877;DRZ001302;DRZ002685
|accession_numbers=CAGE;DRX009003;DRR009877;DRZ001302;DRZ002685;DRZ012652;DRZ014035
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:16, 10 August 2017


Name:intestine, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11131
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
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  SAMD00005553
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11131 CAGE DRX009003 DRR009877
Accession ID Mm9

Library idBAMCTSS
CNhs11131 DRZ001302 DRZ002685
Accession ID Mm10

Library idBAMCTSS
CNhs11131 DRZ012652 DRZ014035
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

CNhs11131

00
10
100
1000
10000.0768
10010.0611
10020.0554
1003-0.0124
10040
10050.244
10060
1007-0.0139
10082.192
1009-0.00526
101-0.127
10100
1011-0.0943
10120
10130.27
1014-0.0874
1015-0.381
1016-0.183
10170
10180.578
10190
1020
10200
10210
10220.189
10230
1024-0.011
10250.661
10260
1027-0.0105
10280
10290.521
1030
10300
1031-0.231
10320.694
10330.0398
10340.146
10350.146
1036-0.129
10370
10380.058
10390.0603
1040.321
1040-0.0982
10410.146



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: CNhs11131

Jaspar motifP-value
MA0002.20.0259
MA0003.10.236
MA0004.10.558
MA0006.10.0385
MA0007.10.524
MA0009.10.234
MA0014.10.364
MA0017.13.7894e-24
MA0018.20.0162
MA0019.10.344
MA0024.10.0068
MA0025.10.574
MA0027.10.615
MA0028.10.577
MA0029.10.988
MA0030.10.248
MA0031.10.0774
MA0035.21.03811e-5
MA0038.10.645
MA0039.22.00468e-4
MA0040.10.0224
MA0041.10.35
MA0042.10.93
MA0043.10.079
MA0046.11.36682e-45
MA0047.26.6959e-5
MA0048.10.697
MA0050.13.23669e-6
MA0051.12.21811e-5
MA0052.19.82261e-5
MA0055.10.212
MA0057.10.131
MA0058.10.389
MA0059.10.653
MA0060.10.0105
MA0061.10.602
MA0062.20.729
MA0065.21.41528e-13
MA0066.10.396
MA0067.10.229
MA0068.10.274
MA0069.10.275
MA0070.10.15
MA0071.10.181
MA0072.10.907
MA0073.10.794
MA0074.10.175
MA0076.10.298
MA0077.10.442
MA0078.10.438
MA0079.20.679
MA0080.22.46621e-4
MA0081.10.373
MA0083.10.952
MA0084.10.408
MA0087.10.914
MA0088.10.666
MA0090.10.86
MA0091.10.834
MA0092.10.382
MA0093.10.533
MA0099.20.00145
MA0100.10.0858
MA0101.10.874
MA0102.20.367
MA0103.15.90173e-6
MA0104.20.0585
MA0105.10.459
MA0106.10.312
MA0107.10.758
MA0108.20.147
MA0111.10.956
MA0112.23.69009e-5
MA0113.10.543
MA0114.14.60054e-30
MA0115.13.86876e-11
MA0116.10.532
MA0117.10.979
MA0119.10.0135
MA0122.10.693
MA0124.10.363
MA0125.10.313
MA0131.10.384
MA0135.10.811
MA0136.16.46362e-4
MA0137.20.995
MA0138.20.33
MA0139.10.0284
MA0140.10.0412
MA0141.13.12728e-5
MA0142.10.148
MA0143.10.0856
MA0144.10.127
MA0145.10.00191
MA0146.10.272
MA0147.10.102
MA0148.19.83186e-7
MA0149.10.0194
MA0150.10.48
MA0152.10.181
MA0153.11.00364e-35
MA0154.10.0468
MA0155.10.525
MA0156.10.0147
MA0157.10.435
MA0159.10.00834
MA0160.10.00863
MA0162.10.367
MA0163.10.168
MA0164.10.914
MA0258.10.0163
MA0259.10.194



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: CNhs11131

Novel motifP-value
10.219
100.283
1000.757
1010.834
1020.674
1030.232
1040.713
1050.42
1060.00877
1070.0365
1080.887
1090.0586
110.193
1100.331
1110.201
1120.0329
1130.767
1140.0701
1150.681
1160.444
1170.481
1180.529
1190.109
120.789
1200.743
1210.994
1220.599
1230.224
1240.844
1250.679
1260.0794
1270.565
1280.0477
1290.309
130.00118
1300.712
1310.0264
1320.602
1330.526
1340.654
1350.454
1360.118
1370.476
1380.471
1390.0702
140.546
1400.368
1410.17
1420.597
1430.15
1440.414
1450.149
1460.205
1470.163
1480.138
1490.791
150.188
1500.292
1510.37
1520.0353
1530.911
1540.5
1550.413
1560.126
1570.755
1580.757
1590.625
1600.262
1610.482
1620.867
1630.247
1640.1
1650.282
1660.987
1670.949
1680.806
1690.00718
170.0739
180.183
190.0481
20.2
200.69
210.888
220.345
230.262
240.845
250.759
260.00875
270.544
280.488
290.345
30.251
300.32
310.649
320.0358
330.171
340.814
350.743
360.968
370.0245
380.321
390.206
40.463
400.306
410.678
420.603
430.273
440.449
450.275
460.27
470.469
480.356
490.175
50.589
500.572
510.603
520.0547
530.967
540.548
550.663
560.364
570.974
580.263
590.182
60.599
600.0311
610.235
620.304
630.17
640.769
650.154
660.485
670.0762
680.236
690.657
70.0842
700.0613
710.152
720.509
730.0859
740.914
750.142
760.715
770.104
780.0374
790.801
80.281
800.704
810.602
820.108
830.139
840.457
850.0336
860.145
870.294
880.832
890.265
90.709
900.21
910.244
920.485
930.651
940.5
950.105
960.985
970.321
980.705
990.0765



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: CNhs11131


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal 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)
0011481 (mouse intestine- 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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