Personal tools

FF:370-44C7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 9: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|datafreeze_phase=1
|datafreeze_phase=1
|def=
|def=
Line 44: Line 45:
|is_obsolete=
|is_obsolete=
|library_id=CNhs11009
|library_id=CNhs11009
|library_id_phase_based=1:CNhs11009
|name=pituitary gland, embryo E13
|name=pituitary gland, embryo E13
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:14, 18 June 2014


Name:pituitary gland, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11009
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage13 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  DRS008931
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11009 CAGE DRX009068 DRR009942
Accession ID Mm9

Library idBAMCTSS
CNhs11009 DRZ001367 DRZ002750
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

CNhs11009

00
10.0356
100
1000.0999
10000
1001-0.0395
10020.251
1003-0.0731
10040.377
10050
1006-2.404932e-4
10070.141
10080
1009-0.0786
101-0.0813
10100
1011-0.0178
10120
1013-0.138
10140.383
10150.358
10160.247
10170
10180
10190
1020
10200
10210.0528
1022-0.0704
10230
10240.0101
10250
10260
10270
10280
1029-0.148
1030.0683
10300
10310.374
1032-0.177
10330.0859
10340
10350
10360.152
10370
1038-0.0488
1039-0.0702
1040
10400.0134
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: CNhs11009

Jaspar motifP-value
MA0002.20.0106
MA0003.10.973
MA0004.10.661
MA0006.10.339
MA0007.10.636
MA0009.10.464
MA0014.10.36
MA0017.18.28548e-6
MA0018.20.305
MA0019.10.723
MA0024.10.017
MA0025.10.164
MA0027.10.284
MA0028.10.115
MA0029.10.0915
MA0030.10.243
MA0031.10.124
MA0035.20.0637
MA0038.10.254
MA0039.20.338
MA0040.10.414
MA0041.10.36
MA0042.10.949
MA0043.10.0242
MA0046.12.73061e-16
MA0047.20.00327
MA0048.10.498
MA0050.18.36892e-7
MA0051.11.12121e-4
MA0052.16.99843e-6
MA0055.10.0287
MA0057.10.129
MA0058.10.654
MA0059.10.832
MA0060.14.49789e-15
MA0061.10.0426
MA0062.20.631
MA0065.20.00315
MA0066.10.11
MA0067.10.0257
MA0068.10.48
MA0069.10.622
MA0070.10.716
MA0071.10.348
MA0072.10.0873
MA0073.10.964
MA0074.10.391
MA0076.10.0573
MA0077.10.0114
MA0078.10.402
MA0079.20.333
MA0080.24.46986e-9
MA0081.10.415
MA0083.10.054
MA0084.10.174
MA0087.10.23
MA0088.10.271
MA0090.10.2
MA0091.10.654
MA0092.10.558
MA0093.10.68
MA0099.28.4466e-4
MA0100.10.899
MA0101.10.207
MA0102.20.381
MA0103.10.528
MA0104.20.337
MA0105.10.522
MA0106.10.139
MA0107.10.0349
MA0108.20.857
MA0111.10.954
MA0112.23.2139e-5
MA0113.10.947
MA0114.11.03346e-4
MA0115.10.0162
MA0116.10.747
MA0117.10.101
MA0119.10.0108
MA0122.10.455
MA0124.10.632
MA0125.10.00947
MA0131.10.643
MA0135.10.00366
MA0136.11.28535e-4
MA0137.20.0831
MA0138.20.0195
MA0139.10.815
MA0140.10.124
MA0141.10.0151
MA0142.10.798
MA0143.10.00446
MA0144.10.116
MA0145.10.352
MA0146.10.406
MA0147.10.267
MA0148.17.30044e-6
MA0149.10.0137
MA0150.14.84486e-5
MA0152.10.618
MA0153.14.24745e-12
MA0154.10.0145
MA0155.10.328
MA0156.10.0214
MA0157.10.23
MA0159.10.0385
MA0160.10.0345
MA0162.10.506
MA0163.10.956
MA0164.10.579
MA0258.17.59046e-4
MA0259.10.687



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: CNhs11009

Novel motifP-value
10.0316
100.204
1000.66
1010.675
1020.744
1030.126
1040.902
1050.18
1060.0118
1070.0252
1080.995
1090.66
110.299
1100.295
1110.0445
1120.0849
1130.401
1140.168
1150.838
1160.894
1170.536
1180.979
1190.28
120.98
1200.931
1210.887
1220.491
1230.151
1240.867
1250.343
1260.877
1270.133
1280.0774
1290.211
130.0925
1300.399
1310.338
1320.576
1330.651
1340.435
1350.168
1360.327
1370.51
1380.706
1390.013
140.362
1400.0145
1410.0542
1420.00375
1430.846
1440.9
1450.335
1460.357
1470.465
1480.361
1490.512
150.0909
1500.525
1510.0918
1520.685
1530.419
1540.168
1550.887
1567.45976e-4
1570.743
1580.217
1590.24
1600.438
1610.741
1620.492
1630.0981
1640.0658
1650.198
1660.852
1670.239
1680.419
1690.373
170.163
180.679
190.214
20.977
200.631
210.564
220.53
230.0989
240.923
250.142
260.378
270.781
280.362
290.398
30.423
300.907
310.615
320.258
330.637
340.678
350.484
360.561
370.0682
380.329
390.874
40.741
400.956
410.645
420.967
430.142
440.537
450.621
460.2
470.209
480.192
490.101
50.0446
500.665
510.463
520.325
530.701
540.352
550.936
560.776
570.272
580.233
590.379
60.784
600.0675
610.869
620.087
630.269
640.963
650.305
660.16
670.607
680.399
690.879
70.118
700.0089
710.239
720.735
730.584
740.274
750.69
760.746
770.449
780.0548
790.365
80.445
800.148
810.376
820.467
830.295
840.759
850.0721
860.557
870.226
880.484
890.301
90.376
900.178
910.457
920.0672
930.215
940.302
950.983
960.272
970.686
980.792
990.669



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: CNhs11009


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)
0000293 (mouse embryonic day 13 sample)
0011325 (mouse pituitary gland- embryo E13 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:370-44C7&oldid=3267117"