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|library_id=CNhs13078
|library_id=CNhs13078
|library_id_phase_based=2:CNhs13078
|library_id_phase_based=2:CNhs13078
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.nobarcode.rdna.fa.gz
|name=Mouse hepatocyte, donor1
|name=Mouse hepatocyte, donor1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 16:30, 17 May 2017


Name:Mouse hepatocyte, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13078
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexNA
ageNA
cell typehepatocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNA2060
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004776
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13078 CAGE DRX008857 DRR009729
Accession ID Mm9

Library idBAMCTSS
CNhs13078 DRZ001154 DRZ002539
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

CNhs13078

00
10
100
1000
10000
1001-0.0394
1002-0.116
10030.00925
10040
10050
1006-0.143
1007-0.481
10080
1009-0.19
1010.0841
10100
1011-0.126
10120
10130.306
1014-0.0874
1015-0.303
1016-0.379
10170
10180
10190
1020
10200.289
10210
10220.303
10230
1024-0.0776
10250
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.775
1032-0.43
10330.225
10340.285
10350
10360.0729
10370
1038-0.219
10390.505
1040
1040-0.538
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: CNhs13078

Jaspar motifP-value
MA0002.20.089
MA0003.10.68
MA0004.10.197
MA0006.10.57
MA0007.10.038
MA0009.10.982
MA0014.10.214
MA0017.18.66483e-14
MA0018.20.514
MA0019.10.998
MA0024.11.64244e-4
MA0025.10.019
MA0027.10.845
MA0028.10.981
MA0029.10.337
MA0030.10.0459
MA0031.10.00211
MA0035.20.0284
MA0038.10.0033
MA0039.20.471
MA0040.10.78
MA0041.10.314
MA0042.10.792
MA0043.10.37
MA0046.15.458e-63
MA0047.21.08072e-5
MA0048.10.246
MA0050.10.553
MA0051.10.243
MA0052.10.548
MA0055.10.297
MA0057.10.42
MA0058.10.134
MA0059.10.00703
MA0060.11.94261e-9
MA0061.10.333
MA0062.20.587
MA0065.26.37281e-12
MA0066.10.0171
MA0067.10.508
MA0068.10.431
MA0069.10.126
MA0070.10.317
MA0071.13.38577e-5
MA0072.10.00241
MA0073.10.919
MA0074.10.165
MA0076.10.601
MA0077.10.165
MA0078.10.478
MA0079.20.0959
MA0080.20.00182
MA0081.10.164
MA0083.10.159
MA0084.10.534
MA0087.10.481
MA0088.10.959
MA0090.10.354
MA0091.10.846
MA0092.10.306
MA0093.10.239
MA0099.21.48312e-6
MA0100.10.961
MA0101.10.508
MA0102.20.272
MA0103.10.0355
MA0104.20.118
MA0105.10.0621
MA0106.10.11
MA0107.10.803
MA0108.20.46
MA0111.10.741
MA0112.22.20028e-5
MA0113.10.175
MA0114.11.33348e-14
MA0115.11.07137e-9
MA0116.10.049
MA0117.10.213
MA0119.10.113
MA0122.10.458
MA0124.10.807
MA0125.10.249
MA0131.10.871
MA0135.10.874
MA0136.10.0147
MA0137.20.048
MA0138.20.478
MA0139.10.165
MA0140.10.902
MA0141.11.84412e-5
MA0142.10.305
MA0143.10.167
MA0144.10.12
MA0145.10.148
MA0146.10.0664
MA0147.10.0639
MA0148.13.21286e-7
MA0149.10.00335
MA0150.19.07196e-6
MA0152.10.537
MA0153.11.09216e-44
MA0154.10.16
MA0155.10.984
MA0156.10.0589
MA0157.10.0133
MA0159.13.17121e-4
MA0160.15.06551e-6
MA0162.10.375
MA0163.10.00109
MA0164.10.984
MA0258.16.94323e-4
MA0259.10.418



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: CNhs13078

Novel motifP-value
10.0963
100.261
1000.276
1010.915
1020.789
1030.0214
1040.492
1050.765
1060.0118
1070.0561
1080.664
1090.0853
110.0871
1100.0639
1110.00253
1120.0203
1130.764
1140.00365
1150.383
1160.915
1170.0453
1180.585
1190.0822
120.443
1200.827
1210.584
1220.658
1230.443
1240.287
1250.486
1260.221
1270.622
1280.00666
1290.79
130.0014
1300.0461
1310.905
1320.428
1330.197
1340.691
1350.408
1360.438
1370.793
1380.838
1390.187
140.837
1400.219
1410.117
1420.426
1430.285
1440.433
1450.15
1460.566
1470.423
1480.842
1490.408
150.153
1500.247
1510.525
1520.0878
1530.692
1540.89
1550.547
1560.319
1570.806
1580.538
1590.615
1600.396
1610.83
1620.364
1630.255
1640.0802
1650.651
1660.82
1670.413
1680.713
1690.00245
170.0547
180.399
190.189
20.966
200.363
210.792
220.198
230.194
240.319
250.546
260.00836
270.829
280.334
290.158
30.116
300.986
310.268
320.0487
330.234
340.804
350.18
360.0908
370.0536
380.448
390.314
40.631
400.14
410.525
420.518
430.0855
440.00167
450.686
460.0615
470.507
480.225
490.0534
50.168
500.868
510.237
520.419
530.507
540.257
550.913
560.48
570.761
580.306
590.184
60.678
600.0701
610.375
620.0776
630.133
640.537
650.253
660.554
670.709
680.108
690.921
70.267
700.0133
710.0191
720.933
730.0247
740.839
750.009
760.382
770.255
780.013
790.682
80.0123
800.813
810.841
820.0321
830.207
840.049
850.0678
860.101
870.164
880.954
890.2
90.927
900.412
910.621
920.0457
930.44
940.815
950.148
960.369
970.649
980.476
990.393



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: CNhs13078


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)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000109 (mouse hepatocyte 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:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)

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