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{{f5samples
{{f5samples
|id=FF:406-44C5
|id=406
|name=adrenal gland, embryo E14
|name=adrenal gland, embryo E14
|sample_id=406
|sample_id=FF:406-44C5
|rna_tube_id=44C5
|rna_tube_id=44C5
|rna_box=44
|rna_box=44

Revision as of 17:06, 27 February 2012


Name:adrenal gland, embryo E14
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 stage14 days embryo
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
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

CNhs11038

00
10
100
1000
10000
1001-0.0365
10020.499
1003-0.0446
10040
1005-0.138
10060.0695
1007-0.00314
10080
10090.0289
1010.0858
10100
10110.0475
10120
1013-0.117
10140.315
10150.161
10160.287
10170
10180
10190
1020
10200
1021-0.0487
1022-0.0545
10230
10240.00214
10250.0717
10260.0108
10270.0695
10280
1029-0.0535
1030.37
10300
10310.365
1032-0.017
10330.0653
10340
10350
10360.128
10370
1038-0.0567
10390.00745
1040
1040-0.0023
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 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: CNhs11038

Jaspar motifP-value
MA0002.20.00393
MA0003.10.83
MA0004.10.434
MA0006.10.371
MA0007.10.925
MA0009.10.0835
MA0014.10.518
MA0017.15.92242e-4
MA0018.20.921
MA0019.10.82
MA0024.12.86489e-9
MA0025.10.0869
MA0027.13.1015e-4
MA0028.10.553
MA0029.10.00353
MA0030.10.00292
MA0031.10.0024
MA0035.20.0355
MA0038.10.0549
MA0039.20.215
MA0040.10.0292
MA0041.10.145
MA0042.10.258
MA0043.10.788
MA0046.19.68521e-5
MA0047.21.40509e-4
MA0048.10.0032
MA0050.11.34247e-5
MA0051.11.09077e-7
MA0052.15.18523e-5
MA0055.10.0126
MA0057.10.115
MA0058.10.71
MA0059.10.464
MA0060.18.56563e-10
MA0061.10.275
MA0062.20.375
MA0065.20.00197
MA0066.10.0629
MA0067.10.284
MA0068.10.427
MA0069.10.363
MA0070.10.254
MA0071.10.246
MA0072.10.322
MA0073.10.966
MA0074.10.743
MA0076.10.635
MA0077.10.125
MA0078.10.77
MA0079.20.807
MA0080.21.52226e-7
MA0081.10.454
MA0083.10.843
MA0084.10.331
MA0087.10.238
MA0088.10.838
MA0090.10.353
MA0091.10.643
MA0092.10.785
MA0093.10.451
MA0099.20.0406
MA0100.10.824
MA0101.10.45
MA0102.20.0122
MA0103.13.57053e-6
MA0104.20.666
MA0105.10.678
MA0106.10.241
MA0107.10.127
MA0108.20.827
MA0111.10.571
MA0112.20.0038
MA0113.10.626
MA0114.10.00246
MA0115.10.195
MA0116.10.786
MA0117.10.456
MA0119.10.777
MA0122.10.71
MA0124.10.412
MA0125.10.0458
MA0131.10.914
MA0135.10.762
MA0136.16.81303e-5
MA0137.20.0224
MA0138.20.0463
MA0139.10.128
MA0140.11.22867e-4
MA0141.10.776
MA0142.10.707
MA0143.10.0729
MA0144.10.155
MA0145.10.0357
MA0146.10.706
MA0147.10.615
MA0148.10.00479
MA0149.10.12
MA0150.10.0453
MA0152.10.797
MA0153.12.92312e-5
MA0154.10.109
MA0155.10.899
MA0156.10.00226
MA0157.10.00539
MA0159.10.0105
MA0160.10.178
MA0162.10.746
MA0163.10.367
MA0164.10.844
MA0258.10.00479
MA0259.10.728



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: CNhs11038

Novel motifP-value
10.0997
100.212
1000.867
1010.832
1020.848
1030.195
1040.821
1050.42
1060.0303
1070.318
1080.723
1090.369
110.47
1100.857
1110.0317
1120.258
1130.319
1140.045
1150.733
1160.795
1170.393
1180.467
1190.0761
120.616
1200.338
1210.84
1220.763
1230.973
1240.63
1250.0655
1260.244
1270.366
1280.0271
1290.107
130.183
1300.438
1310.814
1320.336
1330.285
1340.319
1350.533
1360.755
1370.858
1380.368
1390.0138
140.132
1400.13
1410.33
1420.745
1430.283
1440.407
1450.748
1460.776
1470.601
1480.218
1490.689
150.115
1500.821
1510.0445
1520.518
1530.567
1540.538
1550.912
1562.8089e-7
1570.158
1580.087
1590.0869
1600.98
1610.721
1620.91
1630.0379
1640.344
1650.0814
1660.589
1670.476
1680.535
1690.166
170.204
180.778
190.816
20.938
200.865
210.641
220.604
230.234
240.739
250.298
260.481
270.528
280.0995
290.64
30.576
300.871
310.531
320.975
330.667
340.912
350.106
360.582
370.203
380.693
390.575
40.706
400.915
410.0218
420.84
430.283
440.47
450.254
460.237
470.353
480.345
490.0961
50.142
500.533
510.64
520.334
530.898
540.409
550.225
560.689
570.854
580.0728
590.813
60.578
600.0673
610.405
620.087
630.347
640.982
650.401
660.621
670.889
680.141
690.623
70.125
703.90236e-4
710.416
720.486
730.212
740.512
750.425
760.922
770.426
780.313
790.28
80.852
800.15
810.544
820.272
830.57
840.114
850.0137
860.605
870.978
880.913
890.0838
90.581
900.328
910.37
920.285
930.213
940.98
950.597
960.887
970.836
980.364
990.82



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: CNhs11038


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)
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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