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{{f5samples
{{f5samples
|id=FF:430-45I2
|id=FF:430-45I2
|name=thymus, embryo E15, biol_rep1
|name=thymus, embryo E15
|sample_id=430
|sample_id=430
|rna_tube_id=430-45I2
|rna_tube_id=45I2
|rna_box=430-45I2
|rna_box=45
|rna_position=430-45I2
|rna_position=I2
|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=CNhs11005,LSID730,,COMPLETED
|profile_hcage=CNhs11005,LSID730,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:54, 27 February 2012


Name:thymus, embryo E15
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage15 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

CNhs11005

00
10
100
1000
1000-0.0142
10010
10020.189
1003-0.0125
10040
10050
1006-0.145
10070.0533
10080
1009-0.0572
1010.163
10100
10110.0706
10120.111
1013-0.169
10140.284
10150.074
1016-0.0682
10170
10180.46
10190
1020
10200
10210.0395
1022-0.143
10230
10240.0212
10250.0745
10260
10270.0425
10280
10290.0324
1030.159
10300
1031-9.683218e-5
1032-0.141
10330
10340.0425
10350
10360.311
10370
1038-0.216
1039-0.0565
1040
1040-0.0397
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: CNhs11005

Jaspar motifP-value
MA0002.20.0119
MA0003.10.936
MA0004.10.681
MA0006.10.916
MA0007.10.43
MA0009.10.971
MA0014.10.526
MA0017.10.00124
MA0018.26.66521e-7
MA0019.10.782
MA0024.11.19813e-9
MA0025.11.35368e-4
MA0027.10.161
MA0028.14.49841e-5
MA0029.10.85
MA0030.10.0173
MA0031.10.00534
MA0035.20.182
MA0038.10.997
MA0039.20.598
MA0040.10.392
MA0041.10.0601
MA0042.10.289
MA0043.10.00957
MA0046.11.28915e-23
MA0047.20.00983
MA0048.10.0801
MA0050.11.05613e-4
MA0051.10.00404
MA0052.15.08832e-7
MA0055.10.0384
MA0057.10.605
MA0058.10.775
MA0059.10.00732
MA0060.10.00218
MA0061.11.79787e-6
MA0062.21.22171e-10
MA0065.20.15
MA0066.10.259
MA0067.10.0658
MA0068.10.377
MA0069.10.499
MA0070.10.784
MA0071.10.0056
MA0072.10.0544
MA0073.10.729
MA0074.10.949
MA0076.13.89133e-5
MA0077.10.144
MA0078.10.393
MA0079.20.169
MA0080.27.86969e-12
MA0081.10.0088
MA0083.10.0574
MA0084.10.853
MA0087.10.602
MA0088.10.0377
MA0090.10.127
MA0091.10.0927
MA0092.10.878
MA0093.10.731
MA0099.20.0342
MA0100.10.414
MA0101.18.16913e-7
MA0102.20.17
MA0103.10.0359
MA0104.20.0424
MA0105.11.11311e-7
MA0106.10.177
MA0107.12.33638e-7
MA0108.20.0341
MA0111.10.789
MA0112.20.0938
MA0113.10.657
MA0114.12.19525e-4
MA0115.10.0997
MA0116.10.00122
MA0117.10.176
MA0119.10.844
MA0122.10.873
MA0124.10.576
MA0125.10.543
MA0131.10.0764
MA0135.10.266
MA0136.15.50819e-15
MA0137.20.0114
MA0138.22.33684e-6
MA0139.10.0501
MA0140.10.344
MA0141.10.00294
MA0142.10.578
MA0143.10.669
MA0144.10.262
MA0145.10.551
MA0146.10.472
MA0147.10.00556
MA0148.10.0164
MA0149.10.566
MA0150.10.00957
MA0152.10.612
MA0153.15.7686e-8
MA0154.10.0231
MA0155.10.373
MA0156.19.99895e-19
MA0157.10.0539
MA0159.10.699
MA0160.10.00138
MA0162.10.113
MA0163.11.6284e-4
MA0164.10.848
MA0258.10.473
MA0259.10.351



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: CNhs11005

Novel motifP-value
10.91
100.0335
1000.967
1010.799
1020.508
1030.339
1040.905
1050.772
1060.553
1070.662
1080.729
1090.149
110.119
1100.0755
1110.551
1120.271
1130.49
1140.207
1150.881
1160.391
1170.0323
1180.476
1190.925
120.307
1200.612
1210.926
1220.935
1230.627
1240.931
1250.377
1260.913
1270.959
1280.448
1290.375
130.0077
1300.197
1310.776
1320.399
1330.177
1340.242
1350.283
1360.787
1370.00282
1380.971
1390.193
140.174
1400.691
1410.846
1420.73
1430.0896
1440.654
1450.0159
1460.888
1470.201
1480.531
1490.723
150.687
1500.277
1510.972
1520.583
1530.188
1540.387
1550.381
1561.08945e-5
1570.242
1580.279
1590.872
1600.149
1610.382
1620.264
1630.138
1640.0972
1650.554
1660.691
1670.361
1680.165
1690.344
170.71
180.842
190.716
20.387
200.388
210.0324
220.915
230.297
240.0732
250.542
260.00237
270.463
280.244
290.0559
30.384
300.335
310.231
320.423
330.88
340.744
350.717
360.457
370.211
380.193
390.939
40.911
400.28
410.344
420.0686
430.818
440.573
450.902
460.262
470.763
480.415
490.994
50.744
500.0345
510.82
520.545
530.54
540.111
550.784
560.806
570.436
580.275
590.167
60.271
600.663
610.0535
620.344
630.736
640.456
650.353
660.945
670.861
680.266
690.89
70.377
700.496
719.95694e-4
720.303
730.335
740.449
750.129
760.209
770.923
780.409
790.679
80.488
800.277
810.958
820.95
830.942
840.00566
850.104
860.555
870.368
880.175
890.471
90.752
900.503
910.497
920.213
930.657
940.442
950.327
960.346
970.303
980.412
990.753



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: CNhs11005


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)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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