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|is_obsolete=
|is_obsolete=
|library_id=CNhs13407
|library_id=CNhs13407
|library_ids=CNhs13407
|name=TSt-4/DLL1 feeder cells, biol_rep1
|name=TSt-4/DLL1 feeder cells, biol_rep1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:09, 25 October 2013


Name:TSt-4/DLL1 feeder cells, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13407
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  DRS008771
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13407 CAGE DRX008908 DRR009782
Accession ID Mm9

Library idBAMCTSS
CNhs13407 DRZ001207 DRZ002590
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

CNhs13407

00
10
100
1000
10000
1001-0.0668
10020.361
1003-0.102
10040
10050
1006-0.143
10070.315
10080
10090.882
101-0.0812
10100
1011-0.337
10120
10130.115
1014-0.0874
1015-0.00444
10160.405
10170
10180
10190
1020
10200
10210
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280.359
1029-0.115
1030.321
10300
10310.0949
1032-0.184
1033-0.0752
10340
10350
10360.0168
10370
10380.554
10390.0102
1040
10400.883
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: CNhs13407

Jaspar motifP-value
MA0002.21.92641e-4
MA0003.10.765
MA0004.10.59
MA0006.10.207
MA0007.10.594
MA0009.10.304
MA0014.10.246
MA0017.10.123
MA0018.20.72
MA0019.10.999
MA0024.10.00964
MA0025.10.925
MA0027.10.495
MA0028.10.805
MA0029.10.543
MA0030.10.579
MA0031.10.845
MA0035.26.39194e-4
MA0038.10.116
MA0039.20.148
MA0040.10.991
MA0041.10.755
MA0042.10.493
MA0043.10.441
MA0046.13.71484e-5
MA0047.20.844
MA0048.10.00485
MA0050.10.0156
MA0051.10.0222
MA0052.11.71128e-4
MA0055.10.148
MA0057.10.502
MA0058.10.441
MA0059.10.796
MA0060.18.48182e-5
MA0061.10.0759
MA0062.20.709
MA0065.20.841
MA0066.10.291
MA0067.10.165
MA0068.10.164
MA0069.10.57
MA0070.10.2
MA0071.10.5
MA0072.10.22
MA0073.10.591
MA0074.10.797
MA0076.10.843
MA0077.10.246
MA0078.10.00548
MA0079.20.147
MA0080.20.961
MA0081.10.238
MA0083.10.00462
MA0084.10.182
MA0087.10.682
MA0088.10.00544
MA0090.11.98238e-5
MA0091.10.23
MA0092.10.257
MA0093.10.676
MA0099.23.4467e-4
MA0100.10.0839
MA0101.10.294
MA0102.20.00734
MA0103.11.60612e-6
MA0104.20.188
MA0105.10.0186
MA0106.13.06164e-6
MA0107.10.215
MA0108.21.97756e-4
MA0111.10.518
MA0112.20.179
MA0113.10.833
MA0114.10.0752
MA0115.10.199
MA0116.10.303
MA0117.10.494
MA0119.10.0103
MA0122.10.635
MA0124.10.238
MA0125.10.0967
MA0131.10.868
MA0135.10.181
MA0136.10.254
MA0137.20.183
MA0138.20.00463
MA0139.10.623
MA0140.10.00195
MA0141.10.448
MA0142.10.906
MA0143.10.029
MA0144.10.0892
MA0145.10.17
MA0146.10.0481
MA0147.10.169
MA0148.10.852
MA0149.10.379
MA0150.10.0395
MA0152.10.664
MA0153.15.37938e-4
MA0154.10.0673
MA0155.10.849
MA0156.10.832
MA0157.10.0727
MA0159.10.794
MA0160.10.609
MA0162.10.0942
MA0163.10.342
MA0164.10.977
MA0258.10.294
MA0259.10.969



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: CNhs13407

Novel motifP-value
10.185
100.0374
1000.448
1010.675
1020.356
1030.428
1040.92
1050.222
1060.198
1070.25
1080.897
1090.228
110.214
1100.0308
1110.513
1120.5
1130.428
1140.173
1150.456
1160.244
1170.00158
1180.705
1190.894
120.257
1200.353
1210.89
1220.909
1230.652
1240.206
1250.146
1260.494
1270.105
1280.183
1290.0692
130.428
1300.792
1310.186
1320.795
1330.802
1340.75
1350.216
1360.168
1370.252
1380.516
1390.737
140.951
1400.877
1410.283
1420.72
1430.0503
1440.0368
1450.112
1460.922
1470.432
1480.819
1490.273
150.392
1500.0511
1510.921
1520.191
1530.678
1540.401
1550.609
1560.0635
1570.564
1580.851
1590.125
1600.721
1610.249
1620.924
1630.56
1640.0092
1650.884
1660.526
1670.465
1680.49
1690.0132
170.174
180.207
190.169
20.755
200.124
210.0435
220.147
230.609
240.583
250.895
260.00495
270.451
280.891
290.0823
30.0448
300.554
310.439
320.888
330.816
340.743
350.664
360.415
370.0622
380.315
390.212
40.197
400.69
410.155
420.264
430.118
440.485
450.71
460.156
470.306
480.693
490.196
50.247
500.875
510.626
520.705
530.689
540.973
550.294
560.575
570.0217
580.816
590.0978
60.763
600.151
610.492
620.435
630.557
640.788
650.635
660.291
670.441
680.44
690.175
70.125
700.0274
710.00407
720.561
730.0404
740.21
750.0424
760.408
770.173
780.0409
790.362
80.6
800.171
810.203
820.138
830.25
840.645
850.185
860.52
870.171
880.613
890.427
90.494
900.00158
910.0442
920.21
930.00574
940.123
950.932
960.575
970.128
980.264
990.944



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: CNhs13407


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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