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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1830
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1830
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1830
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1830
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.cell_line.hCAGE/mouse%2520fibroblast%2520cell%2520line%253a%2520CRL-1658%2520NIH%252f3T3.CNhs11093.1830-49C7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.cell_line.hCAGE/mouse%2520fibroblast%2520cell%2520line%253a%2520CRL-1658%2520NIH%252f3T3.CNhs11093.1830-49C7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.cell_line.hCAGE/mouse%2520fibroblast%2520cell%2520line%253a%2520CRL-1658%2520NIH%252f3T3.CNhs11093.1830-49C7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.cell_line.hCAGE/mouse%2520fibroblast%2520cell%2520line%253a%2520CRL-1658%2520NIH%252f3T3.CNhs11093.1830-49C7.mm10.nobarcode.ctss.bed.gz

Revision as of 18:27, 4 August 2017


Name:mouse fibroblast cell line: CRL-1658 NIH/3T3
Species:Mouse (Mus musculus)
Library ID:CNhs11093
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNIH/Swiss
tissuewhole body
dev stageembryo
sexunknown_sex_type
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005849
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11093 CAGE DRX008760 DRR009632
Accession ID Mm9

Library idBAMCTSS
CNhs11093 DRZ001057 DRZ002442
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11093

00
10
100
1000
10000.0659
1001-0.0195
10020.0797
10030.291
10040
10050
1006-0.143
1007-0.0134
10080
10090.349
1010.177
10100
1011-0.175
10120
1013-0.102
1014-0.0851
10150.183
10160.0736
10170
10180
10190
1020
10200
10210.0172
1022-0.124
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.148
1030.215
10300
10310.242
1032-0.111
1033-0.0752
10340
10350
1036-0.0597
10370
1038-0.23
1039-0.0742
1040
10400.411
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: CNhs11093

Jaspar motifP-value
MA0002.20.631
MA0003.10.75
MA0004.10.115
MA0006.10.547
MA0007.10.64
MA0009.10.665
MA0014.10.709
MA0017.10.0104
MA0018.20.707
MA0019.10.417
MA0024.10.0112
MA0025.10.454
MA0027.10.195
MA0028.10.00199
MA0029.10.374
MA0030.10.0511
MA0031.10.171
MA0035.29.98939e-4
MA0038.10.276
MA0039.20.11
MA0040.10.178
MA0041.10.57
MA0042.10.712
MA0043.10.143
MA0046.11.17976e-8
MA0047.20.0658
MA0048.14.58889e-5
MA0050.10.456
MA0051.10.946
MA0052.12.38173e-4
MA0055.12.66278e-4
MA0057.10.742
MA0058.10.052
MA0059.10.0198
MA0060.10.682
MA0061.10.561
MA0062.20.012
MA0065.20.308
MA0066.10.74
MA0067.10.72
MA0068.10.304
MA0069.10.606
MA0070.10.14
MA0071.10.986
MA0072.10.888
MA0073.10.346
MA0074.10.783
MA0076.10.022
MA0077.10.148
MA0078.10.0186
MA0079.20.284
MA0080.20.00342
MA0081.10.418
MA0083.10.537
MA0084.10.588
MA0087.10.996
MA0088.10.073
MA0090.10.0375
MA0091.10.468
MA0092.10.69
MA0093.10.17
MA0099.22.72436e-9
MA0100.10.0101
MA0101.10.102
MA0102.20.417
MA0103.13.19984e-4
MA0104.20.051
MA0105.10.644
MA0106.10.00728
MA0107.10.408
MA0108.21.44633e-7
MA0111.10.537
MA0112.20.602
MA0113.10.844
MA0114.10.0475
MA0115.10.298
MA0116.10.387
MA0117.10.895
MA0119.10.494
MA0122.10.902
MA0124.10.689
MA0125.10.00793
MA0131.10.192
MA0135.10.696
MA0136.10.419
MA0137.20.578
MA0138.25.07383e-4
MA0139.10.12
MA0140.10.00101
MA0141.10.608
MA0142.10.416
MA0143.10.516
MA0144.10.587
MA0145.10.275
MA0146.10.0084
MA0147.10.0567
MA0148.10.194
MA0149.10.392
MA0150.10.0157
MA0152.10.97
MA0153.15.01577e-8
MA0154.10.298
MA0155.10.634
MA0156.10.29
MA0157.10.777
MA0159.10.478
MA0160.10.673
MA0162.10.467
MA0163.10.0502
MA0164.10.241
MA0258.10.79
MA0259.10.0544



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: CNhs11093

Novel motifP-value
10.561
100.176
1000.716
1010.0799
1020.783
1030.422
1040.711
1050.539
1060.475
1070.119
1080.792
1090.202
110.186
1100.0311
1110.321
1120.668
1130.335
1140.609
1150.726
1160.0642
1179.28766e-4
1180.747
1190.353
120.943
1200.448
1210.477
1220.182
1230.329
1240.0235
1250.187
1260.423
1270.333
1280.358
1290.436
130.474
1300.339
1310.196
1320.31
1330.13
1340.705
1350.429
1360.933
1370.746
1380.713
1390.0322
140.397
1400.921
1410.872
1420.74
1430.012
1440.649
1450.118
1460.125
1470.88
1480.55
1490.481
150.702
1500.0601
1510.96
1520.104
1530.951
1540.571
1550.171
1560.793
1570.499
1580.548
1590.0285
1600.916
1610.527
1620.983
1630.668
1640.00139
1650.362
1660.489
1670.944
1680.639
1690.0487
170.78
180.0261
190.645
20.106
200.0185
210.0221
220.748
230.269
240.258
250.969
260.0375
270.288
280.427
290.0286
30.656
300.272
310.68
320.639
330.91
340.22
350.41
360.937
370.027
380.856
390.607
40.399
400.048
410.264
420.36
430.915
440.474
450.253
460.723
470.875
480.792
490.601
50.736
500.956
510.735
520.45
530.278
540.304
550.5
560.488
570.205
580.394
590.531
60.685
600.816
610.464
620.87
630.627
640.928
650.83
660.417
670.824
680.161
690.388
70.975
700.138
710.066
720.967
730.0113
740.41
750.033
760.0506
770.699
780.0919
790.113
80.109
800.0418
810.879
820.715
830.436
840.36
850.934
860.272
870.292
880.373
890.215
90.694
900.0443
910.444
920.741
930.0848
940.394
950.0118
960.781
970.584
980.705
990.422



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: CNhs11093


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
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011287 (mouse fibroblast cell line: CRL-1658 NIH/3T3 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
NA

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