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{{f5samples
{
|DRA_sample_Accession=CAGE@DRS008773
|accession_numbers=CAGE;DRX008910;DRR009784;DRZ001209;DRZ002592
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:

Revision as of 13:45, 21 October 2013


Name:TSt-4/DLL1 feeder cells, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs13409
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008773
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13409 CAGE DRX008910 DRR009784
Accession ID Mm9

Library idBAMCTSS
CNhs13409 DRZ001209 DRZ002592
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

CNhs13409

00
10
100
1000
10000
1001-0.0749
1002-0.0941
1003-0.175
10040
1005-0.182
1006-0.387
10070.859
10080
10091.089
101-0.386
10100
1011-0.337
10120
10130
1014-0.0874
10150.0708
10161.098
10170
10180
10190
1020
10200
1021-0.0487
1022-0.124
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280.909
1029-0.176
1030
10300
10310.282
1032-0.343
1033-0.0752
10340
10350
1036-0.57
10370
10380.993
1039-0.146
1040
10401.043
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



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: CNhs13409

Jaspar motifP-value
MA0002.27.6061e-5
MA0003.10.716
MA0004.10.791
MA0006.10.429
MA0007.10.503
MA0009.10.674
MA0014.10.712
MA0017.10.521
MA0018.20.0211
MA0019.10.849
MA0024.10.0224
MA0025.10.649
MA0027.10.523
MA0028.16.53286e-8
MA0029.10.824
MA0030.10.548
MA0031.10.918
MA0035.20.77
MA0038.10.0039
MA0039.28.96027e-5
MA0040.10.734
MA0041.10.271
MA0042.10.604
MA0043.10.0143
MA0046.10.194
MA0047.20.41
MA0048.10.401
MA0050.10.0233
MA0051.10.0226
MA0052.10.953
MA0055.10.333
MA0057.10.792
MA0058.10.954
MA0059.10.519
MA0060.11.99934e-15
MA0061.10.0483
MA0062.22.26006e-10
MA0065.20.12
MA0066.10.00777
MA0067.10.483
MA0068.10.87
MA0069.10.492
MA0070.10.175
MA0071.10.0867
MA0072.10.0412
MA0073.10.979
MA0074.10.234
MA0076.12.16229e-6
MA0077.10.619
MA0078.10.0127
MA0079.20.0741
MA0080.20.479
MA0081.10.0971
MA0083.10.096
MA0084.10.454
MA0087.10.415
MA0088.10.112
MA0090.10.00855
MA0091.10.0576
MA0092.10.112
MA0093.10.972
MA0099.20.023
MA0100.10.376
MA0101.10.738
MA0102.20.92
MA0103.10.754
MA0104.20.448
MA0105.10.0023
MA0106.10.0574
MA0107.10.373
MA0108.20.00111
MA0111.10.49
MA0112.26.68407e-5
MA0113.10.223
MA0114.10.574
MA0115.10.596
MA0116.10.0299
MA0117.10.455
MA0119.10.021
MA0122.10.691
MA0124.10.517
MA0125.10.0249
MA0131.10.0205
MA0135.10.054
MA0136.10.0319
MA0137.20.106
MA0138.20.101
MA0139.10.324
MA0140.10.888
MA0141.10.0127
MA0142.10.579
MA0143.10.00788
MA0144.10.751
MA0145.10.056
MA0146.10.448
MA0147.10.598
MA0148.10.137
MA0149.10.384
MA0150.10.038
MA0152.10.784
MA0153.10.443
MA0154.10.00298
MA0155.10.705
MA0156.10.0106
MA0157.10.31
MA0159.10.143
MA0160.10.0524
MA0162.10.36
MA0163.10.078
MA0164.10.689
MA0258.11.39765e-4
MA0259.10.456



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: CNhs13409

Novel motifP-value
10.177
100.588
1000.861
1010.719
1020.617
1030.318
1040.424
1050.0432
1069.14521e-4
1070.00227
1080.702
1090.941
110.173
1100.15
1110.442
1120.0823
1130.667
1140.0363
1150.205
1160.857
1170.417
1180.626
1190.347
120.972
1200.607
1210.875
1220.689
1230.355
1240.898
1250.0387
1260.173
1270.32
1280.00548
1290.167
130.684
1300.672
1310.311
1320.285
1330.977
1340.839
1350.469
1360.112
1370.493
1380.458
1390.0235
140.667
1400.031
1410.141
1420.909
1430.0056
1440.502
1450.174
1460.959
1470.585
1480.104
1490.0892
150.148
1500.0544
1510.305
1520.221
1530.0979
1540.706
1550.917
1560.766
1570.24
1580.0798
1590.71
1600.146
1610.277
1620.516
1630.333
1640.421
1650.195
1660.403
1670.999
1680.901
1690.0316
170.0953
180.109
190.0754
20.476
200.827
210.207
220.101
230.00559
240.933
250.98
260.0388
270.669
280.812
290.488
30.171
300.982
310.413
320.41
330.836
340.461
350.0729
360.691
370.31
380.294
390.458
40.459
400.816
410.0814
420.323
430.142
440.551
450.483
460.047
470.697
480.734
490.104
50.134
500.843
510.363
520.2
530.57
540.461
550.508
560.708
570.179
580.509
590.0666
60.97
600.0783
610.579
620.217
630.204
640.372
650.129
660.206
670.755
680.0443
690.421
70.389
700.0235
710.129
720.86
730.32
740.617
750.283
760.331
770.106
780.362
790.935
80.152
800.487
810.402
820.0216
830.96
840.13
850.134
860.761
870.341
880.751
890.158
90.359
900.0846
910.0315
920.0252
930.00745
940.00709
950.172
960.199
970.532
980.39
990.668



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: CNhs13409


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002293 (epithelial cell of thymus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0011508 (mouse TSt-4/DLL1 feeder cells sample)

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
CL:0000223 (endodermal cell)

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