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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008748
|DRA_sample_Accession=CAGE@SAMD00005998
|accession_numbers=CAGE;DRX008858;DRR009730;DRZ001155;DRZ002540
|accession_numbers=CAGE;DRX008858;DRR009730;DRZ001155;DRZ002540
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423

Revision as of 20:09, 31 July 2014


Name:Mouse hepatocyte, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12615
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainCD-1
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatocyte
cell lineNA
companyxenotech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberM1000.H15
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005998
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12615 CAGE DRX008858 DRR009730
Accession ID Mm9

Library idBAMCTSS
CNhs12615 DRZ001155 DRZ002540
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

CNhs12615

00
10
100
1000
10000.115
10010.217
1002-0.116
10030.151
10040
10050
1006-0.132
1007-0.282
10080
1009-0.00265
101-0.116
10100
1011-0.275
10120
10130.633
1014-0.0874
1015-0.342
1016-0.261
10170
10180
10190
1020
10200.679
10210
10220.503
10230
1024-0.0899
10250
10260
10270
10280
1029-0.0318
103-0.0887
10300
1031-0.875
1032-0.522
1033-0.0752
10340.787
10350
1036-0.603
10370
1038-0.298
10390.756
1040
1040-0.256
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: CNhs12615

Jaspar motifP-value
MA0002.20.103
MA0003.10.753
MA0004.10.361
MA0006.10.425
MA0007.10.127
MA0009.10.947
MA0014.10.125
MA0017.12.18793e-17
MA0018.23.86816e-4
MA0019.10.901
MA0024.13.47234e-4
MA0025.10.436
MA0027.10.927
MA0028.10.561
MA0029.10.563
MA0030.10.0245
MA0031.10.00697
MA0035.20.0793
MA0038.10.0755
MA0039.20.356
MA0040.10.477
MA0041.10.331
MA0042.10.793
MA0043.10.172
MA0046.14.24853e-75
MA0047.23.20429e-6
MA0048.10.276
MA0050.10.662
MA0051.10.811
MA0052.10.00688
MA0055.10.428
MA0057.10.611
MA0058.10.265
MA0059.10.0147
MA0060.11.95194e-5
MA0061.10.664
MA0062.20.824
MA0065.29.38401e-13
MA0066.10.00707
MA0067.10.225
MA0068.10.427
MA0069.10.149
MA0070.10.278
MA0071.11.58017e-5
MA0072.17.403e-5
MA0073.10.85
MA0074.10.155
MA0076.10.984
MA0077.10.0265
MA0078.10.739
MA0079.20.129
MA0080.25.6211e-5
MA0081.10.133
MA0083.10.00448
MA0084.10.678
MA0087.10.256
MA0088.10.2
MA0090.10.551
MA0091.10.883
MA0092.10.306
MA0093.10.395
MA0099.20.838
MA0100.10.681
MA0101.10.835
MA0102.20.547
MA0103.10.0418
MA0104.20.301
MA0105.10.0137
MA0106.10.023
MA0107.10.37
MA0108.23.83941e-5
MA0111.10.861
MA0112.26.06022e-6
MA0113.10.303
MA0114.14.81164e-17
MA0115.18.63658e-12
MA0116.10.0215
MA0117.10.623
MA0119.10.0462
MA0122.10.177
MA0124.10.807
MA0125.10.441
MA0131.10.86
MA0135.10.551
MA0136.14.21035e-4
MA0137.20.118
MA0138.20.533
MA0139.10.0811
MA0140.10.704
MA0141.11.28718e-6
MA0142.10.27
MA0143.10.164
MA0144.10.414
MA0145.10.158
MA0146.10.0782
MA0147.10.21
MA0148.14.99283e-9
MA0149.10.0041
MA0150.10.00385
MA0152.10.779
MA0153.16.88402e-55
MA0154.10.0956
MA0155.10.823
MA0156.10.0345
MA0157.10.00887
MA0159.15.56982e-4
MA0160.14.14715e-5
MA0162.10.414
MA0163.13.12745e-4
MA0164.10.931
MA0258.13.89487e-4
MA0259.10.951



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: CNhs12615

Novel motifP-value
10.0562
100.105
1000.398
1010.868
1020.302
1030.00282
1040.7
1050.796
1060.105
1070.185
1080.973
1090.0767
110.0586
1100.0549
1110.00141
1120.0135
1130.9
1140.00123
1150.492
1160.989
1170.0755
1180.336
1190.17
120.483
1200.925
1210.934
1220.739
1230.367
1240.43
1250.908
1260.0865
1270.831
1280.0669
1290.875
130.00128
1300.434
1310.982
1320.399
1330.714
1340.997
1350.595
1360.755
1370.905
1380.815
1390.212
140.619
1400.179
1410.44
1420.0509
1430.405
1440.631
1450.15
1460.747
1470.353
1480.482
1490.0671
150.186
1500.261
1510.474
1520.32
1530.435
1540.939
1550.391
1560.723
1570.804
1580.937
1590.804
1600.283
1610.666
1620.304
1630.592
1640.131
1650.753
1660.532
1670.112
1680.99
1690.00194
170.0483
180.633
190.128
20.959
200.41
210.927
220.193
230.294
240.227
250.582
260.00914
270.75
280.437
290.147
30.0794
300.9
310.307
320.122
330.446
340.875
350.117
360.0984
370.0593
380.407
390.247
40.541
400.275
410.961
420.37
430.0808
446.67159e-4
450.879
460.0891
470.334
480.151
490.0476
50.122
500.917
510.337
520.755
530.466
540.4
550.478
560.424
570.421
580.37
590.292
60.811
600.211
610.391
620.0895
630.153
640.447
650.234
660.707
670.72
680.139
690.658
70.245
700.0104
710.0221
720.787
730.112
740.465
750.0111
760.606
770.373
780.0629
790.622
80.0063
800.827
810.88
820.0375
830.379
840.0813
850.0259
860.069
870.581
880.73
890.177
90.929
900.0432
910.371
920.127
930.0991
940.718
950.254
960.204
970.871
980.394
990.255



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: CNhs12615


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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