Personal tools

FF:1393-42G2

From FANTOM5_SSTAR

Revision as of 19:04, 14 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:thymus, neonate N30
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 stage30 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]


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

CNhs11132

00
10
100
1000
1000-0.0115
10010.0738
1002-0.0837
1003-0.116
10040
10050.048
1006-0.143
10070.159
10080
1009-0.19
1010.03
10100
10110.023
10120.567
10130.0207
1014-0.0874
1015-0.0323
1016-0.379
10170
10180.167
10190
1020.131
10200
10210
1022-0.224
10230
1024-0.103
1025-0.0611
10260
10270
10280
10290.39
103-0.0788
10300.048
1031-0.757
1032-0.429
10330.104
10340
10350
10360.0803
10370
1038-0.301
1039-0.0378
1040
1040-0.121
10410.048



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: CNhs11132

Jaspar motifP-value
MA0002.21.82127e-4
MA0003.10.439
MA0004.10.309
MA0006.10.697
MA0007.10.353
MA0009.10.45
MA0014.10.395
MA0017.10.817
MA0018.20.0994
MA0019.10.492
MA0024.10.0569
MA0025.10.0144
MA0027.10.662
MA0028.13.64475e-6
MA0029.10.205
MA0030.10.768
MA0031.10.0349
MA0035.20.44
MA0038.10.274
MA0039.20.454
MA0040.10.513
MA0041.10.325
MA0042.10.905
MA0043.10.147
MA0046.14.57227e-14
MA0047.20.361
MA0048.10.814
MA0050.11.09854e-7
MA0051.12.09528e-6
MA0052.12.02474e-4
MA0055.10.282
MA0057.10.747
MA0058.10.395
MA0059.10.039
MA0060.10.598
MA0061.11.07682e-4
MA0062.22.91989e-19
MA0065.20.695
MA0066.10.0125
MA0067.10.308
MA0068.10.523
MA0069.10.954
MA0070.10.6
MA0071.10.397
MA0072.13.88486e-6
MA0073.10.752
MA0074.10.914
MA0076.12.45594e-8
MA0077.10.0701
MA0078.10.628
MA0079.20.0546
MA0080.27.0926e-14
MA0081.10.0241
MA0083.10.0555
MA0084.10.545
MA0087.10.344
MA0088.10.429
MA0090.10.0397
MA0091.10.0722
MA0092.10.957
MA0093.10.308
MA0099.20.12
MA0100.10.0308
MA0101.16.5061e-4
MA0102.20.494
MA0103.13.52092e-5
MA0104.20.315
MA0105.13.37347e-8
MA0106.10.901
MA0107.16.2943e-4
MA0108.25.44483e-4
MA0111.10.259
MA0112.20.0128
MA0113.10.517
MA0114.10.321
MA0115.10.691
MA0116.10.004
MA0117.10.858
MA0119.10.966
MA0122.10.952
MA0124.10.395
MA0125.10.401
MA0131.10.307
MA0135.10.201
MA0136.16.94065e-24
MA0137.20.1
MA0138.22.53715e-4
MA0139.10.179
MA0140.10.756
MA0141.10.384
MA0142.10.41
MA0143.10.288
MA0144.10.422
MA0145.10.679
MA0146.10.323
MA0147.10.192
MA0148.10.429
MA0149.10.0299
MA0150.10.411
MA0152.10.939
MA0153.11.3443e-8
MA0154.10.115
MA0155.10.934
MA0156.14.22736e-27
MA0157.10.135
MA0159.10.122
MA0160.10.297
MA0162.10.701
MA0163.10.00413
MA0164.10.9
MA0258.10.045
MA0259.10.889



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: CNhs11132

Novel motifP-value
10.157
100.024
1000.77
1010.699
1020.508
1030.222
1040.942
1050.829
1060.717
1070.892
1080.211
1090.319
110.124
1100.0836
1110.744
1120.15
1130.33
1140.386
1150.448
1160.984
1174.70776e-4
1180.154
1190.234
120.672
1200.218
1210.433
1220.978
1230.412
1240.683
1250.152
1260.556
1270.84
1280.533
1290.184
130.0359
1300.312
1310.603
1320.847
1330.989
1340.696
1350.393
1360.341
1370.48
1380.773
1390.248
140.949
1400.992
1410.62
1420.487
1430.225
1440.153
1450.147
1460.709
1470.402
1480.227
1490.883
150.0829
1500.471
1510.0864
1520.204
1530.153
1540.0962
1550.0745
1560.136
1570.732
1580.0841
1590.0554
1600.877
1610.403
1620.697
1630.879
1640.175
1650.298
1660.341
1670.156
1680.242
1690.198
170.605
180.756
190.709
20.094
200.311
210.596
220.996
230.842
240.164
250.22
260.0564
270.314
280.113
290.117
30.103
300.161
310.6
320.131
330.479
340.883
350.0679
360.158
370.116
380.195
390.73
40.773
400.672
410.88
420.0272
430.405
440.887
450.85
460.129
470.394
480.216
490.131
50.224
500.714
510.832
520.152
530.995
540.41
550.444
560.652
570.302
580.182
590.721
60.2
600.985
610.0625
620.0797
630.672
640.832
650.405
660.436
670.787
680.622
690.38
70.136
700.198
710.0782
720.539
730.259
740.784
750.0111
760.0548
770.224
780.175
790.876
80.64
800.0769
810.87
820.605
830.761
840.137
850.929
860.129
870.143
880.415
890.371
90.268
900.0345
910.831
920.968
930.8
940.324
950.436
960.0166
970.546
980.602
990.435



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: CNhs11132


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
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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1393-42G2&oldid=1697224"