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{{f5samples
{{f5samples
|id=FF:420-27D2
|id=FF:420-27D2
|name=whole body, embryo E14.5, biol_rep1
|name=whole body, embryo E14.5
|sample_id=420
|sample_id=420
|rna_tube_id=420-27D2
|rna_tube_id=27D2
|rna_box=420-27D2
|rna_box=27
|rna_position=420-27D2
|rna_position=D2
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs10578,LSID653,,COMPLETED
|profile_hcage=CNhs10578,LSID653,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:59, 27 February 2012


Name:whole body, embryo E14.5
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage14.5 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]





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

CNhs10578

00
10.0945
100
1000.0945
10000.0473
1001-0.0631
10020.143
10030.163
10040.0945
1005-0.00321
10060.0324
10070.0249
10080
10090.108
1010.0567
10100
10110.0929
10120.0945
1013-0.168
10140.298
10150.14
10160.264
10170
10180.345
10190
1020
10200
10210
10220.0241
10230
10240.162
10250.295
10260
10270.238
10280
10290.163
1030.375
10300
10310.446
1032-0.138
10330.0969
10340
10350.0945
10360.144
10370
10380.0122
1039-0.0533
1040
10400.129
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: CNhs10578

Jaspar motifP-value
MA0002.20.00191
MA0003.10.843
MA0004.10.162
MA0006.10.608
MA0007.10.0474
MA0009.10.435
MA0014.10.0536
MA0017.11.97993e-5
MA0018.20.00842
MA0019.10.355
MA0024.10.00707
MA0025.10.0303
MA0027.10.253
MA0028.11.60344e-6
MA0029.10.356
MA0030.10.261
MA0031.10.00139
MA0035.20.234
MA0038.10.00459
MA0039.20.393
MA0040.10.121
MA0041.10.124
MA0042.10.421
MA0043.10.284
MA0046.10.0019
MA0047.20.1
MA0048.10.0494
MA0050.16.90341e-7
MA0051.11.92338e-6
MA0052.11.18698e-5
MA0055.10.00291
MA0057.10.507
MA0058.10.0652
MA0059.10.0237
MA0060.12.64699e-8
MA0061.10.148
MA0062.22.0728e-14
MA0065.24.32013e-5
MA0066.10.188
MA0067.10.0562
MA0068.10.704
MA0069.10.517
MA0070.10.497
MA0071.10.00252
MA0072.10.0148
MA0073.10.743
MA0074.10.0309
MA0076.11.73752e-6
MA0077.10.781
MA0078.10.175
MA0079.20.32
MA0080.22.20951e-7
MA0081.10.0455
MA0083.12.37049e-5
MA0084.10.637
MA0087.10.0754
MA0088.10.133
MA0090.10.631
MA0091.10.774
MA0092.10.772
MA0093.10.193
MA0099.20.00274
MA0100.10.0288
MA0101.10.00463
MA0102.20.498
MA0103.10.00821
MA0104.20.276
MA0105.10.942
MA0106.10.0525
MA0107.10.0203
MA0108.26.65393e-14
MA0111.10.326
MA0112.20.0024
MA0113.10.0886
MA0114.15.62932e-4
MA0115.10.0106
MA0116.10.456
MA0117.10.183
MA0119.10.817
MA0122.10.867
MA0124.10.78
MA0125.10.00313
MA0131.10.814
MA0135.10.553
MA0136.12.22206e-11
MA0137.22.34562e-4
MA0138.20.325
MA0139.10.0205
MA0140.12.29924e-6
MA0141.13.3893e-7
MA0142.10.879
MA0143.10.198
MA0144.10.00304
MA0145.10.253
MA0146.10.00972
MA0147.10.361
MA0148.10.137
MA0149.10.00145
MA0150.10.00346
MA0152.10.318
MA0153.10.0592
MA0154.10.0859
MA0155.10.714
MA0156.13.10263e-11
MA0157.10.00438
MA0159.15.26744e-4
MA0160.13.98178e-5
MA0162.10.931
MA0163.10.0235
MA0164.10.824
MA0258.10.00205
MA0259.10.587



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: CNhs10578

Novel motifP-value
10.0794
100.0609
1000.693
1010.972
1020.0877
1030.0565
1040.767
1050.896
1060.383
1070.509
1080.542
1090.0466
110.0528
1100.142
1110.0127
1120.00981
1130.883
1140.00555
1150.896
1160.633
1170.0047
1180.297
1190.215
120.592
1200.502
1210.411
1220.895
1230.912
1240.795
1250.121
1260.0538
1270.546
1280.856
1290.352
130.00733
1300.388
1310.098
1320.916
1330.45
1340.673
1350.831
1360.00195
1370.504
1380.965
1390.0157
140.606
1400.837
1410.112
1420.34
1430.142
1440.304
1450.165
1460.968
1470.606
1480.199
1490.163
150.0248
1500.678
1510.131
1520.15
1530.462
1540.709
1550.123
1561.42572e-9
1570.673
1580.0632
1590.335
1600.563
1610.186
1620.555
1630.247
1640.0184
1650.104
1660.338
1670.195
1680.27
1690.0856
170.145
180.391
190.829
20.253
200.0539
210.645
220.38
230.993
240.0213
250.277
260.311
270.799
280.425
290.0274
30.175
300.16
310.807
320.728
330.0833
340.936
350.153
360.0704
370.014
380.143
390.525
40.793
400.0465
410.0883
420.475
430.232
440.0334
450.866
460.434
470.318
480.0793
490.114
50.56
500.708
510.712
520.856
530.387
540.943
550.845
560.902
570.523
580.35
590.566
60.602
600.252
610.101
620.169
630.391
640.531
650.153
660.972
670.596
680.498
690.561
70.304
700.00247
710.104
720.186
730.00169
740.847
750.00618
760.0201
770.459
780.0961
790.526
80.116
800.542
810.738
820.0866
830.121
840.396
850.144
860.47
870.0153
880.672
890.82
90.814
900.0606
910.638
920.486
930.109
940.927
950.00307
960.787
970.426
980.5
990.588



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: CNhs10578


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)

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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