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|is_obsolete=
|is_obsolete=
|library_id=CNhs11095
|library_id=CNhs11095
|library_ids=CNhs11095
|name=intestine, neonate N07
|name=intestine, neonate N07
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:00, 25 October 2013


Name:intestine, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11095
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
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  DRS008862
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11095 CAGE DRX008999 DRR009873
Accession ID Mm9

Library idBAMCTSS
CNhs11095 DRZ001298 DRZ002681
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

CNhs11095

00
10
100
1000
10000.112
10010.0408
10020.0987
1003-0.00817
10040
10050.203
1006-0.00622
1007-0.0285
10080.203
10090.189
101-0.0869
10100
10110
10120
10130.197
10140.0788
1015-0.0848
1016-0.111
10170
10180.414
10190
1020
10200
1021-0.0487
10220.00841
10230
10240
10250.869
10260
10270
10280
10290.226
1030.145
10300
10310.0889
10320.36
1033-0.017
10340
10350
1036-0.118
10370
10380.0505
10390.073
1040.101
1040-0.0702
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: CNhs11095

Jaspar motifP-value
MA0002.20.161
MA0003.10.0631
MA0004.10.81
MA0006.10.0375
MA0007.10.512
MA0009.10.285
MA0014.10.866
MA0017.12.45371e-28
MA0018.25.80675e-4
MA0019.10.222
MA0024.10.026
MA0025.10.279
MA0027.10.0915
MA0028.10.0782
MA0029.10.86
MA0030.10.265
MA0031.10.141
MA0035.21.71543e-6
MA0038.10.817
MA0039.28.91859e-5
MA0040.10.214
MA0041.10.755
MA0042.10.612
MA0043.10.00128
MA0046.12.95544e-80
MA0047.23.09732e-6
MA0048.10.842
MA0050.17.35344e-9
MA0051.19.16829e-6
MA0052.14.05783e-4
MA0055.10.0317
MA0057.10.126
MA0058.10.515
MA0059.10.552
MA0060.10.029
MA0061.10.554
MA0062.20.0201
MA0065.26.12927e-13
MA0066.10.164
MA0067.10.384
MA0068.10.579
MA0069.10.0504
MA0070.10.316
MA0071.10.683
MA0072.10.631
MA0073.10.789
MA0074.10.267
MA0076.10.0314
MA0077.10.0848
MA0078.10.152
MA0079.20.22
MA0080.20.00554
MA0081.10.0459
MA0083.10.122
MA0084.10.895
MA0087.10.337
MA0088.10.98
MA0090.10.441
MA0091.10.474
MA0092.10.2
MA0093.10.731
MA0099.20.0139
MA0100.10.0111
MA0101.10.72
MA0102.20.49
MA0103.13.01343e-5
MA0104.20.0955
MA0105.10.585
MA0106.10.97
MA0107.10.714
MA0108.24.20206e-5
MA0111.10.49
MA0112.27.13084e-4
MA0113.10.559
MA0114.12.55266e-33
MA0115.11.17646e-8
MA0116.10.522
MA0117.10.771
MA0119.10.046
MA0122.10.867
MA0124.10.408
MA0125.10.58
MA0131.10.433
MA0135.10.00854
MA0136.10.0626
MA0137.20.599
MA0138.20.718
MA0139.10.0448
MA0140.10.0779
MA0141.10.0292
MA0142.10.106
MA0143.10.0338
MA0144.10.0352
MA0145.10.00827
MA0146.10.183
MA0147.10.0487
MA0148.18.47275e-9
MA0149.10.0574
MA0150.10.973
MA0152.10.805
MA0153.17.98129e-50
MA0154.10.0174
MA0155.10.0369
MA0156.10.13
MA0157.10.214
MA0159.10.0327
MA0160.10.154
MA0162.10.275
MA0163.10.0185
MA0164.10.949
MA0258.10.102
MA0259.10.0577



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: CNhs11095

Novel motifP-value
10.548
100.564
1000.475
1010.651
1020.433
1030.302
1040.75
1050.75
1060.00748
1070.012
1080.589
1090.0985
110.41
1100.649
1110.472
1120.0355
1130.53
1140.588
1150.352
1160.225
1170.974
1180.664
1190.304
120.951
1200.966
1210.39
1220.878
1230.319
1240.924
1250.738
1260.133
1270.803
1280.0404
1290.361
130.00324
1300.497
1310.147
1320.24
1330.368
1340.772
1350.568
1360.0693
1370.891
1380.0707
1390.0968
140.648
1400.762
1410.386
1420.669
1430.0551
1440.336
1450.206
1460.113
1470.999
1480.136
1490.165
150.213
1500.26
1510.453
1520.0208
1530.364
1540.961
1550.575
1560.0757
1570.22
1580.26
1590.646
1600.101
1610.518
1620.265
1630.104
1640.221
1650.316
1660.83
1670.217
1680.165
1690.0244
170.133
180.738
190.0588
20.0439
200.222
210.827
220.242
230.407
240.963
250.93
260.0115
270.371
280.78
290.979
30.506
300.152
310.497
320.0577
330.194
340.366
350.906
360.599
370.0734
380.512
390.233
40.397
400.349
410.464
420.944
430.271
440.791
450.117
460.434
470.653
480.489
490.454
50.549
500.492
510.564
520.021
530.636
540.625
550.352
560.37
570.303
580.529
590.138
60.583
600.0353
610.661
620.738
630.333
640.808
650.305
660.341
670.175
680.922
690.86
70.145
700.181
710.184
720.422
730.153
740.811
750.455
760.202
770.0305
780.0921
790.75
80.664
800.697
810.506
820.17
830.977
840.541
850.115
860.334
870.0638
880.912
890.146
90.591
900.89
910.634
920.383
930.435
940.16
950.339
960.561
970.333
980.894
990.0322



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: CNhs11095


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)
0000313 (mouse neonate N7 sample)
0011411 (mouse intestine- 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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