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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008990
|DRA_sample_Accession=CAGE@SAMD00005219
|accession_numbers=CAGE;DRX009127;DRR010001;DRZ001426;DRZ002809
|accession_numbers=CAGE;DRX009127;DRR010001;DRZ001426;DRZ002809
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001255,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0002323,UBERON:0000489,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0001556,UBERON:0001008
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001255,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0002323,UBERON:0000489,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0001556,UBERON:0001008

Revision as of 22:03, 31 July 2014


Name:urinary bladder, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10481
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueurinary bladder
dev stageadult
sexmale
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  SAMD00005219
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10481 CAGE DRX009127 DRR010001
Accession ID Mm9

Library idBAMCTSS
CNhs10481 DRZ001426 DRZ002809
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

CNhs10481

00
10
100
1000
10000.433
10010.203
10020.0404
10030.137
10040
10050.0378
10060.131
1007-0.0227
10080
10090.479
101-0.0409
10100
1011-0.0286
10120
10130.0764
1014-0.0084
1015-0.211
10160.00527
10170
10180.569
10190
1020
10200
10210
10220.128
10230
10240.204
10250.879
10260
10270
10280.0767
10290.117
1030.142
10300
10310.268
10320.158
10330
10340.211
10350
1036-0.225
10370
10380.137
10390.103
1040
10400.353
10410.911



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: CNhs10481

Jaspar motifP-value
MA0002.20.774
MA0003.10.0767
MA0004.10.239
MA0006.10.192
MA0007.10.517
MA0009.10.581
MA0014.10.373
MA0017.10.0149
MA0018.20.0669
MA0019.10.344
MA0024.11.81159e-10
MA0025.10.709
MA0027.10.84
MA0028.10.00461
MA0029.10.917
MA0030.10.021
MA0031.10.011
MA0035.20.106
MA0038.10.357
MA0039.20.0326
MA0040.10.142
MA0041.10.35
MA0042.10.459
MA0043.10.206
MA0046.17.31234e-4
MA0047.21.0603e-4
MA0048.10.0743
MA0050.14.77429e-7
MA0051.15.20781e-4
MA0052.10.625
MA0055.10.0702
MA0057.10.544
MA0058.10.0793
MA0059.10.0024
MA0060.11.09057e-8
MA0061.10.794
MA0062.22.46182e-4
MA0065.20.43
MA0066.10.405
MA0067.10.855
MA0068.10.108
MA0069.10.807
MA0070.10.757
MA0071.10.0803
MA0072.10.111
MA0073.10.766
MA0074.10.618
MA0076.10.00273
MA0077.10.169
MA0078.10.22
MA0079.20.012
MA0080.20.593
MA0081.10.221
MA0083.17.88648e-22
MA0084.10.797
MA0087.10.678
MA0088.10.548
MA0090.10.00324
MA0091.10.376
MA0092.10.5
MA0093.10.218
MA0099.23.52693e-4
MA0100.10.0142
MA0101.10.911
MA0102.20.888
MA0103.10.736
MA0104.20.0513
MA0105.10.167
MA0106.10.119
MA0107.10.673
MA0108.20.47
MA0111.10.958
MA0112.20.124
MA0113.10.827
MA0114.10.015
MA0115.10.0715
MA0116.10.685
MA0117.10.898
MA0119.10.786
MA0122.10.472
MA0124.10.34
MA0125.10.586
MA0131.10.145
MA0135.10.277
MA0136.10.426
MA0137.20.767
MA0138.20.122
MA0139.10.425
MA0140.13.84257e-4
MA0141.18.35194e-5
MA0142.10.539
MA0143.10.498
MA0144.10.716
MA0145.19.31332e-4
MA0146.10.627
MA0147.10.0137
MA0148.10.0012
MA0149.10.391
MA0150.10.202
MA0152.10.43
MA0153.11.53714e-7
MA0154.10.361
MA0155.10.268
MA0156.10.847
MA0157.10.00321
MA0159.10.998
MA0160.10.0189
MA0162.10.844
MA0163.10.221
MA0164.10.919
MA0258.10.888
MA0259.10.0353



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: CNhs10481

Novel motifP-value
10.496
100.099
1000.0923
1010.604
1020.835
1030.582
1040.322
1050.237
1060.0289
1070.0978
1080.745
1090.838
110.53
1100.82
1110.599
1120.4
1130.531
1140.601
1150.65
1160.209
1170.0233
1180.0762
1190.394
120.487
1200.942
1210.889
1220.709
1230.295
1240.156
1250.398
1260.591
1270.318
1280.0649
1290.181
130.751
1300.199
1310.854
1320.777
1330.637
1340.22
1350.915
1360.693
1370.872
1380.0191
1390.308
140.442
1400.0565
1410.262
1420.994
1430.527
1440.844
1450.629
1460.104
1470.776
1480.866
1490.0426
150.96
1500.375
1510.339
1520.00965
1530.755
1540.631
1550.278
1560.0259
1570.771
1580.425
1590.894
1600.536
1610.911
1620.795
1630.0517
1640.672
1650.704
1660.00113
1670.122
1680.102
1690.0756
170.175
180.281
190.122
20.018
200.0386
210.6
220.329
230.135
240.364
250.0584
260.594
270.467
280.691
290.107
30.414
300.355
310.754
320.508
330.429
340.596
350.198
360.0445
370.469
380.889
390.155
40.295
400.255
410.0757
420.354
430.65
440.304
450.0475
460.616
470.88
480.938
490.888
50.838
500.49
510.712
520.0594
530.105
540.682
550.973
560.901
570.349
580.946
590.383
60.485
600.056
610.851
620.556
630.55
640.685
650.827
660.83
670.609
680.0175
690.948
70.754
700.136
710.377
720.23
730.118
740.532
750.14
760.0341
770.382
780.821
790.914
80.128
800.652
810.174
820.224
830.89
840.618
850.463
860.645
870.632
880.602
890.232
90.231
900.046
910.871
920.308
930.0212
940.0855
950.544
960.686
970.216
980.952
990.602



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: CNhs10481


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)
0007023 (adult organism)
0001255 (urinary bladder)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0001556 (lower urinary tract)
0001008 (renal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011437 (mouse urinary bladder- adult 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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