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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120

Revision as of 16:50, 29 March 2012


Name:hepatoblastoma cell line:HuH-6
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexmale
age1
cell typehepatoblast
cell lineHuH-6
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.014
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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 no result for this sample


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: CNhs11742

Jaspar motifP-value
MA0002.20.14
MA0003.10.465
MA0004.16.025e-4
MA0006.10.625
MA0007.10.382
MA0009.10.217
MA0014.10.711
MA0017.17.10981e-9
MA0018.20.754
MA0019.10.653
MA0024.11.09478e-7
MA0025.10.0557
MA0027.10.719
MA0028.10.564
MA0029.10.0226
MA0030.10.0229
MA0031.10.00521
MA0035.20.017
MA0038.10.00796
MA0039.20.137
MA0040.10.568
MA0041.10.46
MA0042.10.833
MA0043.10.0923
MA0046.11.71966e-31
MA0047.21.35326e-4
MA0048.10.695
MA0050.19.6665e-9
MA0051.13.60972e-6
MA0052.10.922
MA0055.10.0504
MA0057.10.634
MA0058.11.95092e-4
MA0059.10.0359
MA0060.11.06801e-19
MA0061.12.58514e-4
MA0062.20.452
MA0065.26.38715e-4
MA0066.10.404
MA0067.10.411
MA0068.10.0599
MA0069.10.64
MA0070.10.353
MA0071.10.0621
MA0072.10.133
MA0073.10.296
MA0074.10.523
MA0076.10.526
MA0077.10.0144
MA0078.10.775
MA0079.20.131
MA0080.22.02518e-10
MA0081.17.05312e-4
MA0083.10.687
MA0084.10.454
MA0087.10.755
MA0088.10.801
MA0090.10.0691
MA0091.10.123
MA0092.10.0494
MA0093.13.49915e-4
MA0099.20.00225
MA0100.10.133
MA0101.10.131
MA0102.20.755
MA0103.19.03384e-5
MA0104.20.00839
MA0105.12.07702e-6
MA0106.10.825
MA0107.10.0105
MA0108.29.32892e-7
MA0111.10.283
MA0112.20.0458
MA0113.10.247
MA0114.15.88146e-13
MA0115.14.77989e-4
MA0116.10.0017
MA0117.10.682
MA0119.10.269
MA0122.10.621
MA0124.10.156
MA0125.10.459
MA0131.10.617
MA0135.10.556
MA0136.12.40618e-7
MA0137.20.024
MA0138.20.344
MA0139.10.465
MA0140.10.0265
MA0141.10.102
MA0142.10.0341
MA0143.10.615
MA0144.10.0262
MA0145.10.439
MA0146.10.755
MA0147.10.00588
MA0148.18.42325e-4
MA0149.10.887
MA0150.10.235
MA0152.10.986
MA0153.15.73308e-24
MA0154.16.65914e-4
MA0155.10.636
MA0156.13.38082e-6
MA0157.10.119
MA0159.10.898
MA0160.10.0173
MA0162.10.363
MA0163.14.18301e-4
MA0164.10.0146
MA0258.10.38
MA0259.10.22



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: CNhs11742

Novel motifP-value
10.86
100.00628
1000.993
1010.889
1020.902
1030.343
1040.875
1050.908
1060.0012
1070.142
1080.713
1090.12
110.266
1100.288
1110.108
1120.0809
1130.21
1140.0991
1150.0162
1160.211
1170.195
1180.7
1190.164
120.394
1200.453
1210.187
1220.283
1230.412
1240.602
1250.154
1260.308
1270.425
1280.0782
1290.408
130.148
1300.665
1310.163
1320.345
1330.148
1340.0637
1350.0471
1360.379
1370.0524
1380.156
1390.286
140.697
1400.353
1410.0206
1420.847
1430.0132
1440.495
1450.262
1460.671
1470.423
1480.0455
1490.368
150.651
1500.411
1510.657
1520.0819
1530.149
1540.24
1550.301
1560.708
1570.681
1580.549
1590.649
160.294
1600.883
1610.71
1620.402
1630.966
1640.0487
1650.627
1660.341
1670.746
1680.757
1690.428
170.429
180.0912
190.348
20.166
200.973
210.288
220.807
230.0869
240.529
250.591
260.508
270.209
280.465
290.87
30.0807
300.981
310.779
320.00149
330.276
340.746
350.718
360.177
370.0176
380.807
390.357
40.345
400.697
410.293
420.704
430.111
440.559
450.518
460.59
470.871
480.613
490.707
50.804
500.696
510.715
520.692
530.627
540.756
550.387
560.675
570.774
580.862
590.0287
60.88
600.526
610.252
620.342
630.423
640.517
650.133
660.0101
670.818
680.00407
690.0993
70.163
705.14154e-4
710.00349
720.0749
730.116
740.674
750.632
760.262
770.125
780.0515
790.00988
80.351
800.381
810.268
820.0212
830.529
840.423
856.92955e-4
860.107
870.658
880.467
890.374
90.0947
900.999
910.351
920.0707
930.428
940.262
950.0297
960.826
970.646
980.849
990.863



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: CNhs11742


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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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