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|library_id=CNhs11190
|library_id=CNhs11190
|library_id_phase_based=2:CNhs11190
|library_id_phase_based=2:CNhs11190
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.nobarcode.rdna.fa.gz
|name=pituitary gland, neonate N00
|name=pituitary gland, neonate N00
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:35, 17 May 2017


Name:pituitary gland, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11190
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage0 day neonate
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  SAMD00004923
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11190 CAGE DRX009073 DRR009947
Accession ID Mm9

Library idBAMCTSS
CNhs11190 DRZ001372 DRZ002755
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

CNhs11190

00
10.128
100
1000
10000
1001-0.0749
10020
10030.203
10040.244
1005-0.0389
10060.17
1007-0.258
10080
10090.0165
101-0.15
10100
10110.115
10120
10130.157
10140.441
10150.106
10160.24
10170
10180
10190
1020
10200
10210.115
10220.0573
10230
10240.192
10250
10260.086
10270
10280
1029-0.0674
1030.394
10300
10310.441
10320.0282
10330.14
10340
10350
1036-0.0932
10370
10380.0276
10390.0487
1040
10400.174
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: CNhs11190

Jaspar motifP-value
MA0002.20.0222
MA0003.10.646
MA0004.10.517
MA0006.10.704
MA0007.10.0132
MA0009.10.495
MA0014.10.399
MA0017.12.51495e-9
MA0018.22.65857e-4
MA0019.10.816
MA0024.10.641
MA0025.10.406
MA0027.10.891
MA0028.10.192
MA0029.10.73
MA0030.10.141
MA0031.10.127
MA0035.20.0622
MA0038.10.345
MA0039.20.841
MA0040.10.313
MA0041.10.103
MA0042.10.364
MA0043.16.99592e-4
MA0046.11.86597e-12
MA0047.20.0354
MA0048.10.0315
MA0050.10.201
MA0051.10.67
MA0052.10.134
MA0055.10.661
MA0057.10.519
MA0058.10.521
MA0059.10.0814
MA0060.10.0025
MA0061.10.0815
MA0062.20.0306
MA0065.20.00129
MA0066.10.00447
MA0067.10.859
MA0068.10.346
MA0069.10.166
MA0070.10.338
MA0071.10.136
MA0072.10.0638
MA0073.10.968
MA0074.10.762
MA0076.10.922
MA0077.10.177
MA0078.10.201
MA0079.20.0316
MA0080.22.58426e-6
MA0081.10.313
MA0083.10.747
MA0084.10.443
MA0087.10.967
MA0088.10.0449
MA0090.10.534
MA0091.10.624
MA0092.10.692
MA0093.10.592
MA0099.20.171
MA0100.10.192
MA0101.10.0824
MA0102.20.872
MA0103.10.639
MA0104.20.361
MA0105.10.0209
MA0106.10.0213
MA0107.10.0684
MA0108.20.00229
MA0111.10.816
MA0112.28.09445e-5
MA0113.10.504
MA0114.15.85671e-9
MA0115.11.93184e-6
MA0116.10.0776
MA0117.10.892
MA0119.10.127
MA0122.10.582
MA0124.10.875
MA0125.10.096
MA0131.10.525
MA0135.13.05436e-4
MA0136.11.01554e-5
MA0137.20.246
MA0138.20.157
MA0139.10.445
MA0140.14.99261e-4
MA0141.10.0101
MA0142.10.735
MA0143.10.656
MA0144.10.671
MA0145.10.75
MA0146.10.916
MA0147.10.354
MA0148.10.00607
MA0149.10.0437
MA0150.10.00231
MA0152.10.482
MA0153.11.38151e-10
MA0154.10.126
MA0155.10.22
MA0156.10.00333
MA0157.10.265
MA0159.10.00475
MA0160.10.0187
MA0162.10.298
MA0163.10.11
MA0164.10.87
MA0258.10.00445
MA0259.10.486



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: CNhs11190

Novel motifP-value
10.027
100.0143
1000.925
1010.572
1020.69
1030.0551
1040.691
1050.873
1060.186
1070.18
1080.537
1090.645
110.282
1100.0324
1110.0367
1120.0737
1130.837
1140.38
1150.589
1160.807
1170.00596
1180.245
1190.171
120.847
1200.864
1210.732
1220.182
1230.803
1240.744
1250.333
1260.171
1270.14
1280.314
1290.315
130.00542
1300.716
1310.274
1320.803
1330.427
1340.822
1350.22
1360.0729
1370.688
1380.333
1390.0394
140.928
1400.0112
1410.857
1420.0824
1430.719
1440.627
1450.0916
1460.965
1470.748
1480.406
1490.805
150.0609
1500.418
1510.734
1520.263
1530.481
1540.198
1550.873
1560.00472
1570.383
1580.151
1590.158
1600.194
1610.68
1620.681
1630.172
1640.0356
1650.262
1660.89
1670.038
1680.535
1690.146
170.456
180.744
190.156
20.419
200.464
210.73
220.628
230.571
240.576
250.307
260.00411
270.924
280.319
290.0427
30.157
300.427
310.884
320.941
330.788
340.562
350.281
360.545
370.123
380.617
390.602
40.606
400.823
410.418
420.422
430.0636
440.444
450.966
460.0279
470.29
480.229
490.0562
50.0325
500.77
510.46
520.727
530.828
540.506
550.329
560.868
570.223
580.169
590.853
60.622
600.142
610.0882
620.0692
630.277
640.815
650.633
660.298
670.747
680.28
690.904
70.0401
700.163
710.0142
720.605
730.737
740.109
750.0738
760.292
770.645
780.0022
790.767
80.0533
800.307
810.525
820.454
830.342
840.559
850.0895
860.325
870.0433
880.179
890.231
90.754
900.066
910.294
920.217
930.0135
940.0398
950.798
960.135
970.7
980.828
990.784



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: CNhs11190


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011507 (mouse pituitary gland- neonate N00 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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