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{{f5samples
{{f5samples
|id=FF:1273-19G4
|id=FF:1273-19G4
|name=thymus, embryo E18, biol_rep1
|name=thymus, embryo E18
|sample_id=1273
|sample_id=1273
|rna_tube_id=1273-19G4
|rna_tube_id=19G4
|rna_box=1273-19G4
|rna_box=19
|rna_position=1273-19G4
|rna_position=G4
|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=CNhs10595,LSID654,,COMPLETED
|profile_hcage=CNhs10595,LSID654,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:54, 27 February 2012


Name:thymus, embryo E18
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 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
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

CNhs10595

00
10
100
1000
10000
10010
10020
1003-0.063
10040
10050
1006-0.064
10070.108
10080
1009-0.111
1010.128
10100
10110
10120.254
1013-0.138
10140.109
10150.0493
1016-0.262
10170
10180.0787
10190
1020
10200
10210.145
1022-0.17
10230
1024-0.0112
10250
10260
10270
10280
10290.152
1030
10300
1031-0.331
1032-0.328
10330.0787
10340
10350
10360.189
10370
1038-0.22
1039-0.196
1040
1040-0.0422
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: CNhs10595

Jaspar motifP-value
MA0002.29.71499e-5
MA0003.10.837
MA0004.10.464
MA0006.10.709
MA0007.10.295
MA0009.10.324
MA0014.10.195
MA0017.10.111
MA0018.20.0735
MA0019.10.754
MA0024.18.20631e-6
MA0025.10.00352
MA0027.10.888
MA0028.12.08695e-6
MA0029.10.0827
MA0030.10.466
MA0031.10.297
MA0035.20.815
MA0038.10.422
MA0039.20.503
MA0040.10.444
MA0041.10.8
MA0042.10.736
MA0043.10.343
MA0046.11.54099e-17
MA0047.20.716
MA0048.10.85
MA0050.13.76841e-6
MA0051.13.85684e-6
MA0052.10.122
MA0055.10.711
MA0057.10.615
MA0058.10.605
MA0059.10.0766
MA0060.11.32299e-6
MA0061.11.32032e-6
MA0062.24.81714e-19
MA0065.20.694
MA0066.10.041
MA0067.10.81
MA0068.10.521
MA0069.10.881
MA0070.10.535
MA0071.10.583
MA0072.13.30373e-7
MA0073.10.756
MA0074.10.859
MA0076.11.00861e-8
MA0077.10.323
MA0078.10.756
MA0079.20.0925
MA0080.28.96815e-14
MA0081.10.0145
MA0083.10.606
MA0084.10.526
MA0087.10.549
MA0088.10.137
MA0090.10.0681
MA0091.10.0619
MA0092.10.95
MA0093.10.511
MA0099.20.179
MA0100.10.00868
MA0101.16.64733e-6
MA0102.20.285
MA0103.12.74279e-5
MA0104.20.139
MA0105.18.7407e-9
MA0106.10.786
MA0107.15.2512e-6
MA0108.20.454
MA0111.10.383
MA0112.20.0593
MA0113.10.776
MA0114.10.0555
MA0115.10.354
MA0116.10.00142
MA0117.10.703
MA0119.10.996
MA0122.10.699
MA0124.10.397
MA0125.10.939
MA0131.10.0383
MA0135.10.355
MA0136.11.72414e-23
MA0137.20.0294
MA0138.22.1379e-4
MA0139.10.259
MA0140.10.817
MA0141.10.128
MA0142.10.775
MA0143.10.3
MA0144.10.333
MA0145.10.611
MA0146.10.408
MA0147.10.0673
MA0148.10.758
MA0149.10.242
MA0150.10.264
MA0152.10.953
MA0153.12.46036e-9
MA0154.10.0529
MA0155.10.549
MA0156.17.5479e-29
MA0157.10.518
MA0159.10.0751
MA0160.10.16
MA0162.10.223
MA0163.15.5199e-4
MA0164.10.624
MA0258.10.169
MA0259.10.707



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: CNhs10595

Novel motifP-value
10.493
100.0278
1000.905
1010.925
1020.423
1030.319
1040.553
1050.914
1060.742
1070.726
1080.467
1090.177
110.103
1100.0887
1110.945
1120.302
1130.202
1140.758
1150.466
1160.727
1170.00174
1180.231
1190.534
120.296
1200.242
1210.183
1220.667
1230.433
1240.652
1250.064
1260.947
1270.745
1280.613
1290.372
130.016
1300.304
1310.961
1320.599
1330.899
1340.39
1350.268
1360.7
1370.247
1380.218
1390.987
140.781
1400.774
1410.918
1420.88
1430.114
1440.113
1450.144
1460.618
1470.268
1480.582
1490.804
150.108
1500.279
1510.188
1520.264
1530.31
1540.42
1550.0811
1560.523
1570.628
1580.141
1590.0107
1600.755
1610.401
1620.352
1630.737
1640.271
1650.16
1660.359
1670.532
1680.456
1690.236
170.747
180.878
190.59
20.175
200.592
210.289
220.926
230.893
240.0666
250.258
260.036
270.258
280.248
290.0771
30.344
300.208
310.436
320.0793
330.532
340.511
350.158
360.283
370.261
380.276
390.614
40.727
400.417
410.834
420.0226
430.67
440.777
450.793
460.104
470.356
480.213
490.348
50.321
500.698
510.974
520.262
530.678
540.219
550.362
560.878
570.484
580.224
590.778
60.208
600.997
610.0888
620.0704
630.618
640.543
650.459
660.948
670.793
680.359
690.738
70.0872
700.695
710.0206
720.445
730.397
740.768
750.0483
760.279
770.543
780.0797
790.965
80.619
800.0417
810.897
820.655
830.964
840.322
850.418
860.144
870.303
880.243
890.406
90.246
900.154
910.575
920.311
930.862
940.361
950.326
960.141
970.466
980.423
990.44



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: CNhs10595


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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