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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000153,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002101,UBERON:0002102,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004710,UBERON:0005423,UBERON:0005732,UBERON:0005733
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002102,UBERON:0000926,UBERON:0000479,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0005291,UBERON:0003102,UBERON:0004708,UBERON:0002101,UBERON:0004710,UBERON:0001048,UBERON:0006598,UBERON:0004357,UBERON:0009872,UBERON:0004347,UBERON:0005419,UBERON:0005732,UBERON:0002532,UBERON:0000153,UBERON:0003081,UBERON:0006603,UBERON:0005417,UBERON:0005733,UBERON:0005729
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:26, 8 June 2012


Name:forelimb, embryo E13
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
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
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

CNhs10589

00
10
100
1000
10000
1001-0.0234
10020.0584
10030.208
10040
1005-0.0389
1006-0.0825
10070.114
10080
1009-0.006
1010.103
10100
10110.0498
10120
1013-0.188
10140.218
10150.253
10160.46
10170
10180.231
10190
1020
10200
10210
10220
10230
10240
10250
10260.102
10270.07
10280
10290.173
1030.131
10300
10310.231
1032-0.184
10330.11
10340
10350
10360.177
10370
10380.044
1039-0.194
1040
10400.153
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 no result for this sample


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: CNhs10589

Jaspar motifP-value
MA0002.23.08786e-4
MA0003.10.134
MA0004.10.969
MA0006.10.386
MA0007.10.244
MA0009.10.281
MA0014.10.0905
MA0017.16.1793e-7
MA0018.20.557
MA0019.10.663
MA0024.18.35905e-4
MA0025.10.104
MA0027.10.0991
MA0028.10.575
MA0029.10.967
MA0030.10.155
MA0031.10.0607
MA0035.21.51197e-4
MA0038.10.0395
MA0039.20.0449
MA0040.10.116
MA0041.10.404
MA0042.10.31
MA0043.10.0373
MA0046.15.05515e-19
MA0047.20.00352
MA0048.10.365
MA0050.18.43025e-4
MA0051.10.00143
MA0052.10.92
MA0055.10.283
MA0057.10.14
MA0058.10.97
MA0059.10.598
MA0060.11.84008e-11
MA0061.10.156
MA0062.20.97
MA0065.27.0341e-5
MA0066.10.0786
MA0067.10.45
MA0068.10.348
MA0069.10.393
MA0070.10.77
MA0071.10.0304
MA0072.10.0242
MA0073.10.794
MA0074.10.379
MA0076.10.321
MA0077.10.0699
MA0078.10.657
MA0079.20.419
MA0080.25.49812e-9
MA0081.10.453
MA0083.10.629
MA0084.10.363
MA0087.10.972
MA0088.10.378
MA0090.10.793
MA0091.10.358
MA0092.10.577
MA0093.10.955
MA0099.24.92672e-4
MA0100.10.756
MA0101.10.512
MA0102.20.691
MA0103.10.00265
MA0104.20.919
MA0105.10.00896
MA0106.10.359
MA0107.10.306
MA0108.20.646
MA0111.10.21
MA0112.21.66366e-6
MA0113.10.244
MA0114.17.72762e-5
MA0115.10.00981
MA0116.10.00125
MA0117.10.268
MA0119.10.0381
MA0122.10.593
MA0124.10.316
MA0125.10.094
MA0131.10.303
MA0135.10.285
MA0136.15.5606e-5
MA0137.20.375
MA0138.23.79914e-5
MA0139.10.0153
MA0140.18.7027e-4
MA0141.13.66811e-4
MA0142.10.603
MA0143.10.12
MA0144.10.228
MA0145.10.0422
MA0146.10.302
MA0147.10.95
MA0148.18.71767e-5
MA0149.10.00403
MA0150.16.32051e-4
MA0152.10.104
MA0153.12.99867e-17
MA0154.15.04855e-4
MA0155.10.788
MA0156.10.0977
MA0157.10.281
MA0159.10.00151
MA0160.10.00433
MA0162.10.31
MA0163.10.00234
MA0164.10.96
MA0258.13.01546e-4
MA0259.10.699



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: CNhs10589

Novel motifP-value
10.0587
100.274
1000.994
1010.622
1020.407
1030.0387
1040.651
1050.393
1060.00826
1070.0852
1080.822
1090.0786
110.0918
1100.204
1110.0135
1120.0199
1130.679
1140.0114
1150.426
1160.568
1170.21
1180.502
1190.0406
120.671
1200.42
1210.897
1220.96
1230.104
1240.272
1250.255
1260.349
1270.128
1280.0406
1290.169
130.336
1300.412
1310.385
1320.57
1330.274
1340.657
1350.614
1360.954
1370.536
1380.826
1390.00656
140.327
1400.0301
1410.242
1420.488
1430.363
1440.64
1450.205
1460.531
1470.503
1480.224
1490.32
150.0653
1500.422
1510.0872
1520.157
1530.157
1540.801
1550.488
1560.00194
1570.548
1580.388
1590.598
1600.652
1610.343
1620.935
1630.116
1640.157
1650.138
1660.458
1670.736
1680.569
1690.00461
170.0579
180.241
190.135
20.944
200.977
210.904
220.312
230.227
240.648
250.371
260.333
270.488
280.344
290.295
30.15
300.969
310.294
320.2
330.596
340.676
350.146
360.0677
370.0631
380.375
390.765
40.476
400.213
410.251
420.461
430.121
440.0166
450.548
460.246
470.114
480.115
490.0966
50.119
500.844
510.607
520.315
530.68
540.361
550.315
560.334
570.507
580.276
590.0828
60.515
600.107
610.9
620.0703
630.192
640.37
650.156
660.623
670.69
680.00586
690.315
70.269
706.60004e-4
710.157
720.488
730.134
740.365
750.0446
760.829
770.126
780.366
790.31
80.07
800.138
810.346
820.0783
830.143
840.78
850.0115
860.72
870.292
880.869
890.174
90.626
900.0616
910.353
920.0868
930.734
940.661
950.114
960.15
970.733
980.139
990.541



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: CNhs10589


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)
0000926 (mesoderm)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0003102 (surface structure)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0001048 (primordium)
0006598 (presumptive structure)
0004357 (paired limb/fin bud)
0004347 (limb bud)
0005419 (pectoral appendage bud)
0005732 (limb/fin field)
0002532 (epiblast (generic))
0000153 (anterior region of body)
0003081 (lateral plate mesoderm)
0006603 (presumptive mesoderm)
0005417 (forelimb bud)
0005733 (limb field)
0005729 (forelimb/pectoral fin field)

FF: FANTOM5
NA

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
NA

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