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{{f5samples
{{f5samples
|id=FF:1362-25G7
|id=FF:1362-25G7
|name=thymus, neonate N25, biol_rep1
|name=thymus, neonate N25
|sample_id=1362
|sample_id=1362
|rna_tube_id=1362-25G7
|rna_tube_id=25G7
|rna_box=1362-25G7
|rna_box=25
|rna_position=1362-25G7
|rna_position=G7
|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=CNhs11125,LSID735,,COMPLETED
|profile_hcage=CNhs11125,LSID735,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:54, 27 February 2012


Name:thymus, neonate N25
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 stage25 days neonate
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

CNhs11125

00
10
100
1000
1000-0.0172
10010.0829
1002-0.0696
1003-0.145
10040
10050
1006-0.143
10070.13
10080.0399
1009-0.19
1010.095
10100
10110
10120.544
1013-0.14
1014-0.0874
10150.0637
1016-0.396
10170
10180.0657
10190
1020.0764
10200.00393
10210.0399
1022-0.261
10230
1024-0.0134
1025-0.0611
10260
1027-0.048
10280
10290.359
103-0.0787
10300.0399
1031-0.84
1032-0.447
10330.0349
10340
10350
10360.131
10370
1038-0.337
1039-0.238
1040
1040-0.106
10410.0399



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: CNhs11125

Jaspar motifP-value
MA0002.25.01606e-4
MA0003.10.304
MA0004.10.257
MA0006.10.93
MA0007.10.515
MA0009.10.561
MA0014.10.316
MA0017.10.919
MA0018.20.127
MA0019.10.47
MA0024.10.00256
MA0025.10.0115
MA0027.10.596
MA0028.11.52038e-5
MA0029.10.16
MA0030.10.888
MA0031.10.169
MA0035.20.478
MA0038.10.452
MA0039.20.276
MA0040.10.674
MA0041.10.248
MA0042.10.948
MA0043.10.162
MA0046.11.33716e-13
MA0047.20.586
MA0048.10.758
MA0050.13.84274e-7
MA0051.16.36405e-6
MA0052.12.29389e-4
MA0055.10.706
MA0057.10.751
MA0058.10.371
MA0059.10.015
MA0060.10.266
MA0061.15.78325e-5
MA0062.29.37552e-17
MA0065.20.648
MA0066.10.0133
MA0067.10.364
MA0068.10.535
MA0069.10.894
MA0070.10.522
MA0071.10.353
MA0072.15.26876e-6
MA0073.10.786
MA0074.10.924
MA0076.12.98315e-7
MA0077.10.113
MA0078.10.848
MA0079.20.0341
MA0080.21.38556e-13
MA0081.10.0213
MA0083.10.0339
MA0084.10.392
MA0087.10.392
MA0088.10.339
MA0090.10.0431
MA0091.10.0715
MA0092.10.946
MA0093.10.293
MA0099.20.141
MA0100.10.012
MA0101.13.52519e-4
MA0102.20.623
MA0103.12.26714e-4
MA0104.20.137
MA0105.16.20003e-8
MA0106.10.736
MA0107.14.09203e-4
MA0108.26.68755e-4
MA0111.10.227
MA0112.20.0188
MA0113.10.476
MA0114.10.424
MA0115.10.732
MA0116.10.00323
MA0117.10.759
MA0119.10.856
MA0122.10.989
MA0124.10.374
MA0125.10.36
MA0131.10.229
MA0135.10.138
MA0136.12.03243e-22
MA0137.20.061
MA0138.24.50413e-5
MA0139.10.28
MA0140.10.772
MA0141.10.565
MA0142.10.362
MA0143.10.326
MA0144.10.375
MA0145.10.453
MA0146.10.447
MA0147.10.0618
MA0148.10.538
MA0149.10.0375
MA0150.10.523
MA0152.10.977
MA0153.11.93508e-8
MA0154.10.114
MA0155.10.912
MA0156.19.4547e-26
MA0157.10.326
MA0159.10.135
MA0160.10.434
MA0162.10.662
MA0163.10.00503
MA0164.10.773
MA0258.10.0378
MA0259.10.62



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: CNhs11125

Novel motifP-value
10.158
100.0175
1000.769
1010.834
1020.487
1030.213
1040.828
1050.857
1060.768
1070.813
1080.246
1090.34
110.114
1100.0801
1110.664
1120.144
1130.361
1140.46
1150.581
1160.952
1173.71898e-4
1180.187
1190.204
120.646
1200.135
1210.367
1220.937
1230.524
1240.837
1250.0772
1260.475
1270.754
1280.469
1290.15
130.0277
1300.387
1310.413
1320.769
1330.898
1340.613
1350.457
1360.313
1370.405
1380.684
1390.194
140.883
1400.91
1410.779
1420.338
1430.223
1440.195
1450.0963
1460.815
1470.434
1480.23
1490.901
150.0945
1500.365
1510.193
1520.0849
1530.21
1540.088
1550.106
1560.158
1570.691
1580.0769
1590.0477
1600.875
1610.277
1620.653
1630.934
1640.117
1650.24
1660.427
1670.125
1680.327
1690.4
170.53
180.724
190.657
20.067
200.204
210.553
220.903
230.979
240.225
250.232
260.0373
270.522
280.176
290.0717
30.12
300.138
310.604
320.141
330.534
340.87
350.0438
360.161
370.17
380.244
390.804
40.901
400.608
410.948
420.0365
430.404
440.751
450.74
460.101
470.337
480.184
490.121
50.197
500.757
510.941
520.166
530.917
540.347
550.418
560.739
570.221
580.247
590.698
60.301
600.95
610.0438
620.11
630.566
640.69
650.462
660.443
670.873
680.588
690.69
70.163
700.232
710.0347
720.5
730.442
740.995
750.0173
760.0346
770.294
780.0971
790.621
80.372
800.14
810.922
820.816
830.753
840.132
850.829
860.22
870.124
880.311
890.517
90.311
900.0317
910.914
920.898
930.698
940.199
950.38
960.0125
970.513
980.632
990.357



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: CNhs11125


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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