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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10791-110H8
|fonse_cell_line=FF:10791-110H8
|fonse_cell_line_closure=FF:10791-110H8
|fonse_cell_line_closure=FF:10791-110H8

Revision as of 16:58, 29 March 2012


Name:keratoacanthoma cell line:HKA-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexfemale
age77
cell typeunclassifiable
cell lineHKA-1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.316
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.28
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11880

Jaspar motifP-value
MA0002.20.0188
MA0003.10.0511
MA0004.10.0935
MA0006.10.398
MA0007.10.857
MA0009.10.204
MA0014.10.19
MA0017.10.357
MA0018.20.805
MA0019.10.445
MA0024.10.00884
MA0025.10.873
MA0027.10.382
MA0028.14.33315e-5
MA0029.10.598
MA0030.10.399
MA0031.10.441
MA0035.20.321
MA0038.10.973
MA0039.20.00423
MA0040.10.3
MA0041.10.286
MA0042.10.702
MA0043.10.231
MA0046.10.659
MA0047.20.811
MA0048.10.242
MA0050.18.28422e-6
MA0051.10.00179
MA0052.10.065
MA0055.14.7466e-4
MA0057.10.13
MA0058.10.0276
MA0059.10.186
MA0060.12.52493e-4
MA0061.14.50412e-4
MA0062.26.11221e-6
MA0065.20.805
MA0066.10.966
MA0067.10.222
MA0068.10.694
MA0069.10.497
MA0070.10.671
MA0071.10.44
MA0072.10.922
MA0073.10.897
MA0074.10.923
MA0076.14.0213e-5
MA0077.10.665
MA0078.10.151
MA0079.20.358
MA0080.27.92944e-8
MA0081.10.0594
MA0083.16.85563e-6
MA0084.10.246
MA0087.10.97
MA0088.10.805
MA0090.10.422
MA0091.10.0311
MA0092.10.34
MA0093.10.0741
MA0099.20.73
MA0100.10.571
MA0101.10.00226
MA0102.20.297
MA0103.12.01399e-6
MA0104.20.0493
MA0105.11.04486e-4
MA0106.16.61548e-5
MA0107.11.43991e-4
MA0108.20.00391
MA0111.10.467
MA0112.20.295
MA0113.10.666
MA0114.10.721
MA0115.10.988
MA0116.10.0338
MA0117.10.249
MA0119.10.422
MA0122.10.288
MA0124.10.123
MA0125.10.00911
MA0131.10.162
MA0135.10.989
MA0136.12.79295e-4
MA0137.21.18998e-4
MA0138.20.586
MA0139.10.857
MA0140.10.917
MA0141.10.39
MA0142.10.065
MA0143.10.597
MA0144.10.0313
MA0145.10.693
MA0146.10.338
MA0147.10.144
MA0148.10.251
MA0149.10.0141
MA0150.10.896
MA0152.10.497
MA0153.10.993
MA0154.10.00343
MA0155.10.0583
MA0156.10.0369
MA0157.10.679
MA0159.10.947
MA0160.10.783
MA0162.10.935
MA0163.10.0113
MA0164.10.633
MA0258.10.849
MA0259.10.387



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: CNhs11880

Novel motifP-value
10.441
100.678
1000.107
1010.898
1020.262
1030.55
1040.958
1050.669
1060.317
1070.461
1080.915
1090.00826
110.51
1100.764
1110.436
1120.622
1130.291
1140.774
1150.514
1160.385
1170.585
1180.331
1190.143
120.661
1200.293
1210.468
1220.118
1230.025
1240.0318
1250.727
1260.621
1270.899
1280.363
1290.384
130.00934
1300.764
1310.0767
1320.597
1330.0259
1340.262
1350.0239
1360.00495
1370.0137
1380.474
1390.515
140.984
1400.715
1410.0552
1420.208
1430.106
1440.48
1450.383
1460.0868
1470.871
1480.621
1490.29
150.875
1500.848
1510.938
1520.259
1530.836
1540.598
1550.32
1560.985
1570.947
1580.45
1590.204
160.557
1600.958
1610.501
1620.691
1630.0748
1640.218
1650.82
1660.0608
1670.0666
1680.265
1690.948
170.244
180.195
190.00986
20.607
200.334
210.67
220.526
230.00735
240.189
250.976
260.0583
270.593
280.389
290.401
30.805
300.533
310.586
320.131
330.335
340.199
350.241
360.518
370.745
380.437
390.786
40.773
400.0208
410.143
420.746
430.49
440.0672
450.763
460.939
470.466
480.153
490.369
50.524
500.901
510.948
520.663
530.869
540.674
550.691
560.746
570.22
580.76
590.446
60.678
600.807
610.924
620.488
630.727
640.365
650.896
660.0769
670.753
680.751
690.139
70.48
700.579
710.396
720.672
730.0454
748.51995e-4
750.322
760.949
770.729
780.00457
790.404
80.288
800.313
810.249
820.839
830.276
840.432
850.39
860.142
870.00422
880.926
890.923
90.219
900.27
910.115
920.366
930.684
940.0889
950.0421
960.139
970.893
980.984
990.925



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: CNhs11880


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

DOID: Disease
0050686 (organ system cancer)
0060122 (integumentary system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3149 (keratoacanthoma)
3151 (skin squamous cell carcinoma)
3451 (skin carcinoma)
4 (disease)
4159 (skin cancer)

UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0003102 (surface structure)

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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