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|library_id_phase_based=1:CNhs11008
|name=forelimb, embryo E18
|name=forelimb, embryo E18
|namespace=FANTOM5
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Revision as of 12:02, 18 June 2014


Name:forelimb, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11008
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
dev stage18 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  DRS008832
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11008 CAGE DRX008969 DRR009843
Accession ID Mm9

Library idBAMCTSS
CNhs11008 DRZ001268 DRZ002651
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

CNhs11008

00
10
100
1000
10000.00325
10010.0182
10020
10030.284
10040
10050
1006-0.0587
10070.0367
10080
10090.159
1010.0493
10100
10110
10120
1013-0.0775
10140.518
10150.0133
10160.219
10170
10180.633
10190
1020
10200
1021-0.0487
10220
10230
10240.174
10250
10260
10270.0603
10280
10290.0612
1030.74
10300
10310.409
1032-0.0883
10330
10340
10350
10360.0998
10370
10380.0858
1039-0.14
1040
10400.187
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: CNhs11008

Jaspar motifP-value
MA0002.20.0882
MA0003.10.436
MA0004.10.186
MA0006.10.141
MA0007.10.468
MA0009.10.312
MA0014.10.424
MA0017.11.14219e-14
MA0018.20.00371
MA0019.10.25
MA0024.10.498
MA0025.10.135
MA0027.10.637
MA0028.11.05019e-5
MA0029.10.827
MA0030.10.386
MA0031.10.237
MA0035.26.54672e-7
MA0038.10.641
MA0039.20.0169
MA0040.10.577
MA0041.10.152
MA0042.10.265
MA0043.10.467
MA0046.13.67804e-23
MA0047.20.00999
MA0048.10.956
MA0050.10.0496
MA0051.10.00126
MA0052.14.24141e-4
MA0055.10.0645
MA0057.10.322
MA0058.10.0555
MA0059.10.0624
MA0060.10.411
MA0061.10.402
MA0062.21.27987e-9
MA0065.25.75691e-5
MA0066.10.47
MA0067.10.111
MA0068.10.387
MA0069.10.798
MA0070.10.909
MA0071.11.58942e-4
MA0072.10.0736
MA0073.10.761
MA0074.10.0515
MA0076.16.39201e-6
MA0077.10.413
MA0078.10.0342
MA0079.20.00909
MA0080.27.96946e-7
MA0081.10.00866
MA0083.10.293
MA0084.10.812
MA0087.10.412
MA0088.10.968
MA0090.10.0795
MA0091.10.894
MA0092.10.278
MA0093.10.205
MA0099.21.44464e-4
MA0100.10.0466
MA0101.10.123
MA0102.20.687
MA0103.10.0785
MA0104.20.0828
MA0105.10.809
MA0106.10.0357
MA0107.10.263
MA0108.24.60232e-20
MA0111.10.604
MA0112.20.308
MA0113.10.0359
MA0114.11.25486e-12
MA0115.14.21608e-7
MA0116.10.746
MA0117.10.184
MA0119.10.716
MA0122.10.605
MA0124.10.332
MA0125.10.0218
MA0131.10.963
MA0135.10.943
MA0136.15.21012e-8
MA0137.20.58
MA0138.20.076
MA0139.10.0993
MA0140.11.30915e-4
MA0141.13.74317e-10
MA0142.10.26
MA0143.10.218
MA0144.10.538
MA0145.10.0511
MA0146.10.911
MA0147.10.0659
MA0148.10.0169
MA0149.10.0286
MA0150.10.0103
MA0152.10.0101
MA0153.11.41139e-15
MA0154.10.835
MA0155.10.795
MA0156.15.08451e-5
MA0157.10.272
MA0159.11.63738e-4
MA0160.14.75909e-9
MA0162.10.923
MA0163.10.648
MA0164.10.323
MA0258.10.00952
MA0259.10.489



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: CNhs11008

Novel motifP-value
10.192
100.62
1000.951
1010.55
1020.641
1030.226
1040.0656
1050.591
1060.444
1070.143
1080.734
1090.279
110.126
1100.714
1110.0346
1120.184
1130.945
1140.0654
1150.587
1160.867
1170.0852
1180.0359
1190.379
120.485
1200.554
1210.0626
1220.408
1230.178
1240.418
1250.619
1260.443
1270.867
1280.479
1290.263
130.465
1300.466
1310.863
1320.556
1330.981
1340.701
1350.324
1360.65
1370.858
1380.721
1390.157
140.732
1400.34
1410.396
1420.362
1430.687
1440.291
1450.712
1460.835
1470.322
1480.229
1490.722
150.0168
1500.906
1510.282
1520.0596
1530.779
1540.634
1550.404
1560.124
1570.0176
1580.144
1590.257
1600.0449
1610.686
1620.717
1630.465
1640.307
1650.128
1660.0442
1670.0222
1680.16
1690.118
170.693
180.224
190.525
20.0994
200.176
210.426
220.444
230.126
240.915
250.274
260.0318
270.391
280.4
290.0482
30.205
300.0969
310.306
320.446
330.724
340.608
350.00174
360.0216
370.688
380.693
390.352
40.954
400.0627
410.0652
420.829
430.709
440.0466
450.391
460.727
470.312
480.127
490.0929
50.275
500.267
510.987
520.272
530.286
540.836
550.6
560.786
570.661
580.758
590.763
60.766
600.53
610.793
620.423
630.86
640.216
650.535
660.461
670.681
680.0195
690.682
70.835
700.137
710.867
720.562
730.722
740.836
750.29
760.0272
770.49
780.41
790.642
80.0785
800.0232
810.629
820.417
830.735
840.442
850.686
860.489
870.216
880.922
890.417
90.694
900.27
910.778
920.604
930.532
940.336
950.619
960.721
970.343
980.298
990.235



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: CNhs11008


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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0000302 (mouse embryonic day 18 sample)
0011278 (mouse forelimb- embryo E18 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:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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