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|name=Mouse hepatocyte, donor6
|name=Mouse hepatocyte, donor6
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Revision as of 13:28, 17 June 2014


Name:Mouse hepatocyte, donor6
Species:Mouse (Mus musculus)
Library ID:CNhs13090
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatocyte
cell lineNA
companyNA
collaborationSoichi Kojima (RIKEN ASI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008749
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13090 CAGE DRX008859 DRR009731
Accession ID Mm9

Library idBAMCTSS
CNhs13090 DRZ001156 DRZ002541
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

CNhs13090

00
10
100
1000
10000.0371
10010.162
1002-0.116
10030.254
10040
10050
1006-0.143
1007-0.203
10080
1009-0.0572
101-0.0456
10100
1011-0.298
10120
10130.658
1014-0.0874
1015-0.396
1016-0.377
10170
10180
10190
1020
10200.75
10210
10220.628
10230
1024-0.14
10250.201
10260
10270
10280
1029-0.0989
103-0.0887
10300
1031-0.41
1032-0.395
1033-0.0665
10341.113
10350
1036-0.271
10370
1038-0.276
10390.82
1040
1040-0.216
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: CNhs13090

Jaspar motifP-value
MA0002.20.182
MA0003.10.7
MA0004.10.516
MA0006.10.321
MA0007.10.136
MA0009.10.956
MA0014.10.0738
MA0017.18.87184e-20
MA0018.28.03987e-4
MA0019.10.945
MA0024.11.45855e-4
MA0025.10.28
MA0027.10.9
MA0028.10.548
MA0029.10.329
MA0030.10.0438
MA0031.10.0173
MA0035.20.142
MA0038.10.33
MA0039.20.832
MA0040.10.747
MA0041.10.406
MA0042.10.682
MA0043.10.275
MA0046.11.22483e-70
MA0047.22.26766e-6
MA0048.10.24
MA0050.10.42
MA0051.10.079
MA0052.10.016
MA0055.10.257
MA0057.10.695
MA0058.10.407
MA0059.10.0378
MA0060.12.82413e-6
MA0061.10.514
MA0062.20.988
MA0065.21.43332e-13
MA0066.10.0302
MA0067.10.241
MA0068.10.447
MA0069.10.098
MA0070.10.311
MA0071.13.48778e-5
MA0072.11.23577e-4
MA0073.10.913
MA0074.10.186
MA0076.10.959
MA0077.10.0389
MA0078.10.968
MA0079.20.169
MA0080.20.00639
MA0081.10.27
MA0083.10.00298
MA0084.10.329
MA0087.10.365
MA0088.10.227
MA0090.10.729
MA0091.10.873
MA0092.10.169
MA0093.10.565
MA0099.20.8
MA0100.10.584
MA0101.10.916
MA0102.20.522
MA0103.10.0598
MA0104.20.595
MA0105.10.038
MA0106.10.00865
MA0107.10.614
MA0108.21.17946e-6
MA0111.10.87
MA0112.28.05884e-6
MA0113.10.379
MA0114.11.81009e-18
MA0115.11.32566e-11
MA0116.10.0807
MA0117.10.539
MA0119.10.025
MA0122.10.222
MA0124.10.963
MA0125.10.302
MA0131.10.771
MA0135.10.431
MA0136.10.0266
MA0137.20.0267
MA0138.20.297
MA0139.10.122
MA0140.10.522
MA0141.15.70523e-7
MA0142.10.31
MA0143.10.208
MA0144.10.217
MA0145.10.153
MA0146.10.0825
MA0147.10.43
MA0148.13.22163e-8
MA0149.10.00312
MA0150.10.00593
MA0152.10.467
MA0153.14.15652e-57
MA0154.10.154
MA0155.10.938
MA0156.10.156
MA0157.10.00671
MA0159.14.8844e-4
MA0160.11.79782e-5
MA0162.10.277
MA0163.10.00103
MA0164.10.945
MA0258.10.00159
MA0259.10.92



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: CNhs13090

Novel motifP-value
10.0617
100.151
1000.452
1010.997
1020.294
1030.00526
1040.876
1050.775
1060.125
1070.134
1080.957
1090.0679
110.0628
1100.0382
1110.00343
1120.0192
1130.916
1140.00204
1150.762
1160.92
1170.0633
1180.468
1190.0855
120.431
1200.77
1210.876
1220.56
1230.517
1240.365
1250.82
1260.225
1270.782
1280.0449
1290.749
135.36286e-4
1300.5
1310.715
1320.396
1330.78
1340.909
1350.428
1360.732
1370.855
1380.813
1390.262
140.616
1400.0863
1410.407
1420.0816
1430.536
1440.653
1450.0875
1460.591
1470.461
1480.519
1490.132
150.103
1500.285
1510.457
1520.183
1530.344
1540.875
1550.505
1560.264
1570.924
1580.822
1590.753
1600.257
1610.687
1620.527
1630.33
1640.0827
1650.697
1660.522
1670.0801
1680.822
1690.00159
170.0768
180.81
190.0828
20.953
200.409
210.716
220.172
230.323
240.22
250.502
260.00737
270.787
280.392
290.135
30.0661
300.934
310.392
320.109
330.379
340.836
350.214
360.119
370.0645
380.439
390.245
40.896
400.266
410.996
420.392
430.0778
440.00142
450.833
460.106
470.342
480.173
490.049
50.0921
500.902
510.314
520.626
530.487
540.259
550.621
560.421
570.598
580.352
590.404
60.835
600.185
610.303
620.0969
630.15
640.423
650.256
660.438
670.875
680.122
690.833
70.215
700.0187
710.0342
720.749
730.0714
740.531
750.0108
760.765
770.431
780.0209
790.564
80.0099
800.943
810.756
820.0127
830.352
840.0709
850.0114
860.1
870.45
880.774
890.156
90.981
900.0704
910.581
920.1
930.0389
940.667
950.203
960.373
970.58
980.397
990.165



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: CNhs13090


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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