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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008933
|DRA_sample_Accession=CAGE@SAMD00005651
|accession_numbers=CAGE;DRX009070;DRR009944;DRZ001369;DRZ002752
|accession_numbers=CAGE;DRX009070;DRR009944;DRZ001369;DRZ002752
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949

Revision as of 21:52, 31 July 2014


Name:pituitary gland, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10592
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage15 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005651
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10592 CAGE DRX009070 DRR009944
Accession ID Mm9

Library idBAMCTSS
CNhs10592 DRZ001369 DRZ002752
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

CNhs10592

00
10.105
100
1000.0359
10000
10010.176
10020.0541
1003-0.0308
10040.308
10050
10060.0674
10070.0911
10080
1009-0.0709
101-0.00159
10100
10110.0709
10120
1013-0.013
10140.258
10150.177
10160.192
10170
10180
10190
1020
10200
10210
10220.00785
10230
10240.0954
10250
10260
10270.0709
10280
1029-0.0158
1030.117
10300
10310.41
1032-0.0935
10330.0516
10340
10350
1036-0.028
10370
10380.0257
1039-0.0457
1040
10400.173
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: CNhs10592

Jaspar motifP-value
MA0002.23.00584e-5
MA0003.10.234
MA0004.10.65
MA0006.10.477
MA0007.10.66
MA0009.10.761
MA0014.10.432
MA0017.13.1722e-7
MA0018.20.0168
MA0019.10.605
MA0024.10.132
MA0025.10.903
MA0027.10.758
MA0028.10.269
MA0029.10.385
MA0030.10.554
MA0031.10.843
MA0035.20.0205
MA0038.10.032
MA0039.20.526
MA0040.10.815
MA0041.10.139
MA0042.10.734
MA0043.10.00202
MA0046.18.99287e-20
MA0047.20.0316
MA0048.10.255
MA0050.10.0184
MA0051.10.28
MA0052.11.01935e-4
MA0055.10.721
MA0057.10.124
MA0058.10.599
MA0059.10.115
MA0060.11.41195e-9
MA0061.10.0408
MA0062.20.358
MA0065.25.73721e-5
MA0066.10.00489
MA0067.10.709
MA0068.10.412
MA0069.10.257
MA0070.10.394
MA0071.10.0796
MA0072.10.141
MA0073.10.769
MA0074.10.293
MA0076.10.0636
MA0077.10.195
MA0078.10.571
MA0079.20.158
MA0080.24.05386e-7
MA0081.10.571
MA0083.10.106
MA0084.10.0698
MA0087.10.128
MA0088.10.665
MA0090.10.341
MA0091.10.716
MA0092.10.415
MA0093.10.722
MA0099.26.95472e-4
MA0100.10.989
MA0101.10.233
MA0102.20.98
MA0103.10.507
MA0104.20.676
MA0105.11.80099e-4
MA0106.10.0694
MA0107.10.119
MA0108.20.426
MA0111.10.736
MA0112.25.30851e-8
MA0113.10.726
MA0114.11.41116e-5
MA0115.15.88474e-6
MA0116.10.00324
MA0117.10.659
MA0119.10.0527
MA0122.10.724
MA0124.10.724
MA0125.10.0123
MA0131.10.438
MA0135.10.0426
MA0136.10.00455
MA0137.20.579
MA0138.20.244
MA0139.10.192
MA0140.10.013
MA0141.10.00119
MA0142.10.757
MA0143.10.333
MA0144.10.252
MA0145.10.181
MA0146.10.226
MA0147.10.502
MA0148.10.00532
MA0149.10.00476
MA0150.10.00263
MA0152.10.503
MA0153.11.2216e-14
MA0154.10.00308
MA0155.10.56
MA0156.10.537
MA0157.10.939
MA0159.10.0064
MA0160.10.0129
MA0162.10.259
MA0163.12.51373e-4
MA0164.10.59
MA0258.12.00199e-5
MA0259.10.842



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: CNhs10592

Novel motifP-value
10.0528
100.0665
1000.99
1010.606
1020.853
1030.0924
1040.801
1050.54
1060.0066
1070.0137
1080.599
1090.163
110.103
1100.0941
1110.00772
1120.0387
1130.839
1140.0165
1150.183
1160.364
1170.0629
1180.653
1190.0576
120.921
1200.972
1210.993
1220.536
1230.51
1240.924
1250.144
1260.389
1270.0508
1280.0184
1290.182
130.0437
1300.543
1310.385
1320.563
1330.431
1340.826
1350.28
1360.639
1370.964
1380.499
1390.0434
140.539
1400.0192
1410.591
1420.0666
1430.29
1440.976
1450.0892
1460.664
1470.781
1480.179
1490.312
150.0926
1500.198
1510.271
1520.267
1530.904
1540.41
1550.335
1564.9211e-4
1570.607
1580.266
1590.859
1600.208
1610.591
1620.727
1630.322
1640.0736
1650.143
1660.676
1670.154
1680.786
1691.56263e-4
170.0972
180.268
190.11
20.848
200.869
210.726
220.228
230.147
240.677
250.395
260.0325
270.733
280.562
290.152
30.116
300.959
310.542
320.0893
330.286
340.703
350.377
360.134
370.0681
380.349
390.597
40.402
400.319
410.347
420.428
430.0927
440.0854
450.679
460.0939
470.205
480.135
490.0957
50.0427
500.714
510.476
520.21
530.772
540.411
550.224
560.526
570.227
580.346
590.0682
60.684
600.0403
610.25
620.0865
630.103
640.451
650.165
660.455
670.69
680.0158
690.502
70.109
700.00364
710.0383
720.595
730.136
740.267
750.0925
760.977
770.186
780.0231
790.645
80.0516
800.445
810.346
820.125
830.139
840.82
850.0105
860.473
870.92
880.496
890.231
90.462
900.0931
910.131
920.143
930.117
940.302
950.156
960.102
970.776
980.289
990.626



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: CNhs10592


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)
0000922 (embryo)
0000955 (brain)
0000007 (pituitary gland)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0003296 (gland of diencephalon)
0010133 (neuroendocrine gland)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011345 (mouse pituitary gland- embryo E15 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:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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