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|library_id=CNhs10600
|library_id=CNhs10600
|library_id_phase_based=1:CNhs10600
|name=forelimb, embryo E12
|name=forelimb, embryo E12
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:02, 18 June 2014


Name:forelimb, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10600
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
dev stage12 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  DRS008827
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10600 CAGE DRX008964 DRR009838
Accession ID Mm9

Library idBAMCTSS
CNhs10600 DRZ001263 DRZ002646
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

CNhs10600

00
10
100
1000.0752
10000
10010
10020.0879
10030.0183
10040
1005-0.0651
1006-0.0491
10070.163
10080
1009-0.0572
1010.142
10100
10110.00517
10120
1013-0.151
10140.152
10150.282
10160.556
10170
10180.0752
10190
1020
10200
10210.139
1022-0.0922
10230
1024-0.0899
10250
10260
10270
10280
10290.182
1030.00715
10300
10310.15
1032-0.139
10330.0493
10340
10350
10360.0338
10370
10380.0625
1039-0.216
1040
10400.146
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: CNhs10600

Jaspar motifP-value
MA0002.27.30973e-4
MA0003.10.0599
MA0004.10.861
MA0006.10.379
MA0007.10.468
MA0009.10.296
MA0014.10.0947
MA0017.11.5345e-4
MA0018.20.509
MA0019.10.703
MA0024.15.90299e-5
MA0025.10.147
MA0027.10.24
MA0028.10.552
MA0029.10.925
MA0030.10.18
MA0031.10.0311
MA0035.25.06239e-4
MA0038.10.0168
MA0039.20.00984
MA0040.10.0287
MA0041.10.367
MA0042.10.46
MA0043.10.0264
MA0046.14.89279e-10
MA0047.20.013
MA0048.10.203
MA0050.12.75692e-5
MA0051.14.86594e-4
MA0052.10.392
MA0055.10.219
MA0057.10.0873
MA0058.10.767
MA0059.10.842
MA0060.14.66429e-14
MA0061.10.178
MA0062.20.903
MA0065.23.28993e-4
MA0066.10.146
MA0067.10.509
MA0068.10.63
MA0069.10.737
MA0070.10.935
MA0071.10.038
MA0072.10.0467
MA0073.10.554
MA0074.10.66
MA0076.10.354
MA0077.10.07
MA0078.10.898
MA0079.20.714
MA0080.23.99336e-10
MA0081.10.307
MA0083.10.843
MA0084.10.255
MA0087.10.879
MA0088.10.4
MA0090.10.944
MA0091.10.657
MA0092.10.611
MA0093.10.809
MA0099.24.28602e-5
MA0100.10.477
MA0101.10.533
MA0102.20.622
MA0103.10.00378
MA0104.20.585
MA0105.10.05
MA0106.10.203
MA0107.10.346
MA0108.20.905
MA0111.10.329
MA0112.25.14603e-6
MA0113.10.269
MA0114.10.0012
MA0115.10.174
MA0116.10.00279
MA0117.10.239
MA0119.10.0163
MA0122.10.932
MA0124.10.441
MA0125.10.244
MA0131.10.225
MA0135.10.821
MA0136.13.35915e-5
MA0137.20.328
MA0138.22.27713e-5
MA0139.10.0342
MA0140.10.0175
MA0141.10.00109
MA0142.10.903
MA0143.10.0181
MA0144.10.177
MA0145.10.0265
MA0146.10.371
MA0147.10.716
MA0148.14.36245e-4
MA0149.10.00508
MA0150.10.00185
MA0152.10.108
MA0153.19.16701e-11
MA0154.10.00171
MA0155.10.838
MA0156.10.0357
MA0157.10.126
MA0159.10.00145
MA0160.10.0142
MA0162.10.335
MA0163.10.0079
MA0164.10.831
MA0258.19.11974e-4
MA0259.10.65



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: CNhs10600

Novel motifP-value
10.0577
100.38
1000.798
1010.614
1020.465
1030.0369
1040.942
1050.292
1060.008
1070.115
1080.736
1090.0692
110.102
1100.225
1110.0364
1120.0382
1130.7
1140.0128
1150.337
1160.458
1170.305
1180.842
1190.0372
120.786
1200.356
1210.856
1220.896
1230.0554
1240.143
1250.784
1260.405
1270.113
1280.0411
1290.14
130.452
1300.569
1310.295
1320.36
1330.267
1340.751
1350.395
1360.919
1370.555
1380.746
1390.0076
140.36
1400.0451
1410.325
1420.893
1430.239
1440.763
1450.207
1460.539
1470.467
1480.271
1490.195
150.0729
1500.529
1510.0876
1520.0817
1530.114
1540.973
1550.801
1560.612
1570.793
1580.771
1590.933
1600.69
1610.386
1620.825
1630.081
1640.161
1650.205
1660.309
1670.871
1680.359
1690.00699
170.0543
180.278
190.137
20.712
200.718
210.893
220.273
230.113
240.595
250.46
260.34
270.373
280.354
290.373
30.166
300.777
310.324
320.174
330.651
340.632
350.317
360.119
370.0825
380.306
390.71
40.518
400.183
410.38
420.491
430.141
440.0051
450.533
460.307
470.0849
480.0991
490.124
50.142
500.991
510.528
520.272
530.506
540.382
550.35
560.314
570.502
580.274
590.0474
60.574
600.124
610.731
620.0732
630.128
640.35
650.1
660.559
670.996
680.0427
690.297
70.303
703.09702e-4
710.196
720.358
730.116
740.315
750.11
760.708
770.121
780.418
790.155
80.146
800.0997
810.322
820.0871
830.484
840.778
850.0204
860.66
870.126
880.781
890.131
90.577
900.11
910.397
920.0732
930.326
940.757
950.0943
960.187
970.969
980.22
990.52



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: CNhs10600


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)
0000295 (mouse embryonic day 12 sample)
0011322 (mouse forelimb- embryo E12 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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