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{{f5samples
{{f5samples
|id=FF:49-24D7
|id=49
|name=adrenal gland, adult
|name=adrenal gland, adult
|sample_id=49
|sample_id=FF:49-24D7
|rna_tube_id=24D7
|rna_tube_id=24D7
|rna_box=24
|rna_box=24

Revision as of 17:06, 27 February 2012


Name:adrenal gland, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10508

00
10.0601
100
1000
10000.0993
10010.0498
10020.0227
1003-0.0503
10040
10050.0311
10060.162
1007-0.0614
10080
10090.37
101-0.0018
10100
10110.00281
10120
10130.234
1014-0.0874
1015-0.116
10160.0359
10170
10180
10190
1020
10200
10210
10220.283
10230
10240.0881
10250
10260
10270
10280
10290.0219
103-0.0736
10300
1031-0.037
10320.0482
10330.0599
10340
10350
1036-0.213
10370
10380.12
10390.317
1040
10400.105
10410.802



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 no result for this sample


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: CNhs10508

Jaspar motifP-value
MA0002.20.11
MA0003.10.212
MA0004.10.318
MA0006.10.736
MA0007.10.567
MA0009.10.212
MA0014.10.351
MA0017.10.808
MA0018.20.101
MA0019.10.924
MA0024.11.35738e-9
MA0025.10.0324
MA0027.10.93
MA0028.10.0918
MA0029.10.00713
MA0030.10.389
MA0031.10.21
MA0035.20.496
MA0038.10.611
MA0039.20.164
MA0040.10.324
MA0041.10.323
MA0042.10.889
MA0043.10.409
MA0046.14.43873e-4
MA0047.20.364
MA0048.10.0465
MA0050.13.13063e-9
MA0051.14.90219e-6
MA0052.10.0487
MA0055.15.2659e-4
MA0057.10.689
MA0058.10.443
MA0059.10.0384
MA0060.13.56831e-7
MA0061.10.89
MA0062.20.356
MA0065.20.364
MA0066.10.264
MA0067.10.526
MA0068.10.6
MA0069.10.499
MA0070.10.0127
MA0071.10.188
MA0072.10.118
MA0073.10.748
MA0074.10.604
MA0076.10.19
MA0077.10.17
MA0078.10.0387
MA0079.20.0126
MA0080.20.0246
MA0081.10.252
MA0083.10.972
MA0084.10.247
MA0087.10.453
MA0088.10.775
MA0090.10.601
MA0091.10.204
MA0092.10.513
MA0093.10.464
MA0099.20.0169
MA0100.10.11
MA0101.10.861
MA0102.20.319
MA0103.13.00646e-5
MA0104.20.0939
MA0105.10.0319
MA0106.10.236
MA0107.10.673
MA0108.24.56712e-4
MA0111.10.899
MA0112.20.43
MA0113.10.61
MA0114.10.865
MA0115.10.329
MA0116.10.757
MA0117.10.144
MA0119.10.705
MA0122.10.322
MA0124.10.344
MA0125.10.53
MA0131.10.153
MA0135.10.142
MA0136.10.108
MA0137.20.744
MA0138.20.0184
MA0139.10.705
MA0140.10.419
MA0141.10.184
MA0142.10.601
MA0143.10.436
MA0144.10.894
MA0145.10.164
MA0146.10.156
MA0147.10.0403
MA0148.10.927
MA0149.10.787
MA0150.10.00806
MA0152.10.948
MA0153.18.69554e-8
MA0154.10.28
MA0155.10.724
MA0156.10.0268
MA0157.10.195
MA0159.10.299
MA0160.10.145
MA0162.10.404
MA0163.10.0495
MA0164.10.754
MA0258.10.469
MA0259.10.0418



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: CNhs10508

Novel motifP-value
10.118
100.126
1000.113
1010.108
1020.606
1030.97
1040.728
1050.693
1060.688
1070.715
1080.203
1090.711
110.821
1100.905
1110.792
1120.218
1130.0547
1140.364
1150.0687
1160.0779
1170.0155
1180.985
1190.114
120.884
1200.0084
1210.12
1220.251
1230.248
1240.0199
1250.456
1260.0658
1270.147
1280.445
1290.269
130.0351
1300.275
1310.194
1320.539
1330.855
1340.888
1350.0913
1360.502
1370.562
1380.159
1390.131
140.118
1400.212
1410.398
1420.526
1430.853
1440.976
1450.16
1460.274
1470.69
1480.926
1490.00273
150.369
1500.981
1510.226
1520.0087
1530.673
1540.489
1550.765
1563.6108e-4
1570.229
1580.478
1590.731
1600.601
1610.246
1620.867
1630.206
1640.939
1650.692
1660.336
1670.0721
1680.68
1690.174
170.95
180.788
190.378
20.0382
200.0338
210.591
220.104
230.611
240.281
250.75
260.0177
270.397
280.95
290.0604
30.976
300.493
310.685
320.266
330.0989
340.795
350.779
360.191
370.847
380.272
390.681
40.24
400.613
410.00744
420.795
430.736
440.626
450.512
460.164
470.908
480.657
490.904
50.823
500.983
510.827
520.918
530.147
540.928
550.0326
560.381
570.138
580.794
590.888
60.765
600.928
610.418
620.581
630.844
640.932
650.746
660.277
670.416
680.924
690.476
70.257
700.82
710.00782
720.39
730.156
740.582
750.332
760.532
770.637
780.897
790.319
80.423
800.553
810.123
820.0167
830.0202
840.119
850.802
860.841
870.348
880.513
890.85
90.918
900.251
910.00151
920.634
930.657
940.287
950.613
960.867
970.132
980.68
990.731



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: CNhs10508


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002100 (trunk)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002369 (adrenal gland)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

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
NA

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