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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;449
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;449
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;449
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;449
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.ctss.bed.gz

Revision as of 18:41, 4 August 2017


Name:pituitary gland, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11036
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage16 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  SAMD00004899
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11036 CAGE DRX009071 DRR009945
Accession ID Mm9

Library idBAMCTSS
CNhs11036 DRZ001370 DRZ002753
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11036

00
10.132
100
1000.0713
10000
10010.111
10020.217
10030.109
10040.374
10050
10060.11
10071.901339e-4
10080
10090.116
101-0.064
10100
10110.0713
10120.132
10130.0555
10140.329
10150.172
10160.227
10170
10180
10190
1020
10200
10210
1022-0.0383
10230
10240.132
10250.0714
10260
10270.0431
10280
10290.133
1030.514
10300
10310.552
1032-0.0126
10330.0713
10340
10350
10360.048
10370
10380.0426
1039-0.00758
1040
10400.147
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: CNhs11036

Jaspar motifP-value
MA0002.27.35335e-7
MA0003.10.15
MA0004.10.514
MA0006.10.517
MA0007.10.497
MA0009.10.712
MA0014.10.353
MA0017.11.19637e-9
MA0018.20.0609
MA0019.10.545
MA0024.10.3
MA0025.10.0817
MA0027.10.991
MA0028.10.69
MA0029.10.897
MA0030.10.498
MA0031.10.686
MA0035.20.00112
MA0038.10.231
MA0039.20.258
MA0040.10.124
MA0041.10.446
MA0042.10.753
MA0043.10.0716
MA0046.13.62383e-25
MA0047.28.77191e-4
MA0048.10.373
MA0050.10.00518
MA0051.10.0068
MA0052.12.77157e-7
MA0055.10.956
MA0057.10.113
MA0058.10.448
MA0059.10.177
MA0060.11.59034e-4
MA0061.10.0301
MA0062.20.105
MA0065.22.2187e-6
MA0066.10.0133
MA0067.10.592
MA0068.10.118
MA0069.10.14
MA0070.10.916
MA0071.10.022
MA0072.10.0203
MA0073.10.686
MA0074.10.358
MA0076.10.707
MA0077.10.412
MA0078.10.307
MA0079.20.17
MA0080.21.88611e-9
MA0081.10.184
MA0083.10.104
MA0084.10.0696
MA0087.10.682
MA0088.10.312
MA0090.10.372
MA0091.10.847
MA0092.10.527
MA0093.10.581
MA0099.22.92432e-5
MA0100.10.455
MA0101.10.0689
MA0102.20.981
MA0103.10.393
MA0104.20.501
MA0105.19.55398e-4
MA0106.10.16
MA0107.10.0431
MA0108.20.306
MA0111.10.787
MA0112.22.59777e-7
MA0113.10.876
MA0114.11.36454e-7
MA0115.15.16575e-7
MA0116.10.0123
MA0117.10.54
MA0119.10.106
MA0122.10.669
MA0124.10.374
MA0125.10.0284
MA0131.10.642
MA0135.10.42
MA0136.18.22581e-8
MA0137.20.0349
MA0138.20.528
MA0139.10.221
MA0140.10.00276
MA0141.10.00107
MA0142.10.863
MA0143.10.522
MA0144.10.059
MA0145.10.24
MA0146.10.104
MA0147.10.422
MA0148.12.23136e-4
MA0149.10.00817
MA0150.14.10936e-4
MA0152.10.529
MA0153.15.72728e-20
MA0154.10.00975
MA0155.10.823
MA0156.10.00255
MA0157.10.737
MA0159.15.66226e-4
MA0160.19.52512e-4
MA0162.10.377
MA0163.18.6483e-4
MA0164.10.668
MA0258.14.48369e-5
MA0259.10.78



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: CNhs11036

Novel motifP-value
10.0759
100.0668
1000.992
1010.524
1020.835
1030.134
1040.586
1050.608
1060.013
1070.0601
1080.711
1090.148
110.135
1100.0856
1110.0329
1120.0454
1130.669
1140.0908
1150.627
1160.49
1170.0275
1180.703
1190.0606
120.812
1200.635
1210.564
1220.72
1230.598
1240.809
1250.346
1260.261
1270.0144
1280.0743
1290.33
130.00733
1300.913
1310.644
1320.736
1330.4
1340.765
1350.251
1360.693
1370.615
1380.474
1390.0361
140.573
1400.0528
1410.618
1420.181
1430.97
1440.671
1450.157
1460.463
1470.655
1480.41
1490.366
150.0508
1500.228
1510.276
1520.291
1530.946
1540.655
1550.633
1564.37932e-4
1570.712
1580.202
1590.311
1600.481
1610.559
1620.972
1630.0696
1640.0339
1650.0194
1660.503
1670.238
1680.772
1692.75037e-4
170.126
180.461
190.203
20.976
200.774
210.901
220.28
230.321
240.353
250.276
260.0294
270.593
280.412
290.0813
30.162
300.956
310.603
320.496
330.293
340.829
350.425
360.157
370.0489
380.295
390.662
40.412
400.249
410.0532
420.493
430.0942
440.103
450.588
460.103
470.181
480.0821
490.0904
50.0413
500.839
510.45
520.301
530.935
540.487
550.184
560.613
570.441
580.268
590.147
60.729
600.0384
610.15
620.0611
630.113
640.546
650.175
660.879
670.788
680.0868
690.83
70.0695
700.0118
710.0311
720.468
730.0996
740.39
750.0272
760.975
770.266
780.00834
790.726
80.0432
800.253
810.443
820.121
830.292
840.236
850.0161
860.199
870.357
880.36
890.0941
90.523
900.209
910.265
920.183
930.0675
940.37
950.174
960.274
970.756
980.259
990.84



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: CNhs11036


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)
0000299 (mouse embryonic day 16 sample)
0011353 (mouse pituitary gland- embryo E16 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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