Personal tools

FF:1254-43D6

From FANTOM5_SSTAR

Revision as of 19:19, 17 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:adrenal gland, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11004
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal 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  DRS008792
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11004 CAGE DRX008929 DRR009803
Accession ID Mm9

Library idBAMCTSS
CNhs11004 DRZ001228 DRZ002611
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

CNhs11004

00
10
100
1000
10000.115
10010.0405
10020.438
1003-0.102
10040
1005-0.0465
10060.0227
1007-0.125
10080
10090.0773
1010.0161
10100
1011-0.0912
10120
1013-0.0365
10140.451
1015-0.021
1016-0.0406
10170
10180
10190
1020
10200
1021-0.0487
10220
10230
10240.161
10250.115
10260
10270
10280
10290.105
1030.303
10300
10310.292
1032-0.0238
10330
10340
10350
10360.0542
10370
1038-0.182
10390.0621
1040
10400.0803
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: CNhs11004

Jaspar motifP-value
MA0002.20.278
MA0003.10.239
MA0004.10.00293
MA0006.10.973
MA0007.10.529
MA0009.10.0704
MA0014.10.906
MA0017.10.137
MA0018.20.219
MA0019.10.489
MA0024.10.282
MA0025.10.0367
MA0027.10.0015
MA0028.10.0304
MA0029.16.63752e-6
MA0030.10.0345
MA0031.10.00575
MA0035.20.00956
MA0038.10.584
MA0039.20.993
MA0040.10.00446
MA0041.10.417
MA0042.10.245
MA0043.10.00544
MA0046.10.479
MA0047.20.0368
MA0048.10.737
MA0050.11.95275e-6
MA0051.11.58863e-8
MA0052.10.215
MA0055.10.172
MA0057.10.907
MA0058.10.0135
MA0059.10.636
MA0060.10.561
MA0061.10.392
MA0062.28.45735e-7
MA0065.20.223
MA0066.10.648
MA0067.10.0369
MA0068.10.00943
MA0069.10.037
MA0070.10.0855
MA0071.10.0431
MA0072.10.578
MA0073.10.581
MA0074.10.702
MA0076.10.00252
MA0077.10.288
MA0078.10.536
MA0079.20.831
MA0080.21.44226e-6
MA0081.10.0297
MA0083.10.512
MA0084.10.0877
MA0087.10.0701
MA0088.10.357
MA0090.10.645
MA0091.10.0426
MA0092.10.774
MA0093.10.00681
MA0099.20.735
MA0100.10.0419
MA0101.10.181
MA0102.20.0248
MA0103.16.20356e-7
MA0104.20.451
MA0105.10.0175
MA0106.10.576
MA0107.10.0478
MA0108.20.216
MA0111.10.849
MA0112.20.0539
MA0113.10.537
MA0114.10.821
MA0115.10.426
MA0116.10.0295
MA0117.10.847
MA0119.10.00995
MA0122.10.762
MA0124.10.47
MA0125.10.269
MA0131.10.0585
MA0135.10.603
MA0136.13.12613e-6
MA0137.20.0228
MA0138.20.129
MA0139.10.547
MA0140.14.84934e-7
MA0141.12.35033e-4
MA0142.10.833
MA0143.10.246
MA0144.10.367
MA0145.10.233
MA0146.10.832
MA0147.10.609
MA0148.10.149
MA0149.10.983
MA0150.10.76
MA0152.10.802
MA0153.10.0624
MA0154.10.0146
MA0155.10.245
MA0156.11.54569e-7
MA0157.10.00625
MA0159.10.92
MA0160.10.335
MA0162.10.182
MA0163.10.0133
MA0164.10.966
MA0258.10.198
MA0259.10.47



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: CNhs11004

Novel motifP-value
10.295
100.915
1000.934
1010.529
1020.431
1030.335
1040.794
1050.141
1060.822
1070.154
1080.837
1090.466
110.408
1100.105
1110.487
1120.782
1130.658
1140.953
1150.762
1160.12
1170.496
1180.563
1190.58
120.782
1200.173
1210.384
1220.699
1230.113
1240.127
1250.0702
1260.181
1270.349
1280.615
1290.28
130.718
1300.168
1310.396
1320.336
1330.269
1340.17
1350.0574
1360.388
1370.711
1380.175
1390.395
140.898
1400.501
1410.44
1420.804
1430.0869
1440.053
1450.796
1460.508
1470.396
1480.205
1490.0602
150.56
1500.621
1510.913
1520.585
1530.819
1540.23
1550.733
1561.61369e-5
1570.368
1580.147
1590.621
1600.0754
1610.742
1620.733
1630.795
1640.612
1650.183
1660.403
1670.402
1680.38
1690.0889
170.517
180.0366
190.0527
20.139
200.0482
210.196
220.105
230.793
240.679
250.725
260.816
270.581
280.166
290.98
30.341
300.451
310.675
320.331
330.604
340.404
350.74
360.897
370.462
380.885
390.378
40.614
400.364
410.00393
420.483
430.371
440.329
450.764
460.864
470.582
480.719
490.783
50.677
500.283
510.67
520.763
530.0575
540.794
550.119
560.298
570.523
580.379
590.0588
60.906
600.592
610.138
620.975
630.423
640.299
650.678
660.472
670.524
680.461
690.152
70.766
700.067
710.0841
720.445
730.577
740.583
750.384
760.259
770.288
780.424
790.9
80.191
800.351
810.525
820.0548
830.0754
840.556
850.772
860.745
870.0428
880.471
890.74
90.844
900.52
910.632
920.267
930.473
940.86
950.746
960.26
970.713
980.681
990.12



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: CNhs11004


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)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

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)
0011522 (mouse adrenal 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:0006603 (presumptive mesoderm)
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:1254-43D6&oldid=3078882"