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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:56, 29 March 2012


Name:acantholytic squamous carcinoma cell line:HCC1806
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebreast
dev stageNA
sexfemale
age60
cell typeunclassifiable
cell lineHCC1806
companyATCC
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-penis0.224
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-lymphoma0.608
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11844

Jaspar motifP-value
MA0002.20.00169
MA0003.10.378
MA0004.10.454
MA0006.10.58
MA0007.10.941
MA0009.10.374
MA0014.10.0455
MA0017.10.243
MA0018.20.368
MA0019.10.347
MA0024.17.38702e-8
MA0025.10.436
MA0027.10.607
MA0028.10.41
MA0029.10.664
MA0030.10.869
MA0031.10.785
MA0035.20.508
MA0038.17.97382e-5
MA0039.21.64592e-4
MA0040.10.149
MA0041.10.235
MA0042.10.323
MA0043.10.435
MA0046.10.36
MA0047.20.82
MA0048.10.0409
MA0050.10.131
MA0051.10.0288
MA0052.10.0138
MA0055.11.76462e-4
MA0057.10.417
MA0058.10.702
MA0059.10.763
MA0060.12.75196e-22
MA0061.10.208
MA0062.20.67
MA0065.20.819
MA0066.10.354
MA0067.10.864
MA0068.10.695
MA0069.10.776
MA0070.10.58
MA0071.10.591
MA0072.10.772
MA0073.10.807
MA0074.10.291
MA0076.10.827
MA0077.10.0815
MA0078.10.757
MA0079.20.844
MA0080.21.52078e-6
MA0081.10.00926
MA0083.10.43
MA0084.10.091
MA0087.10.292
MA0088.10.23
MA0090.10.177
MA0091.14.66345e-4
MA0092.10.316
MA0093.10.427
MA0099.20.297
MA0100.10.652
MA0101.10.77
MA0102.20.242
MA0103.17.25164e-6
MA0104.20.297
MA0105.10.0596
MA0106.10.031
MA0107.10.397
MA0108.20.0743
MA0111.10.863
MA0112.20.111
MA0113.10.113
MA0114.10.964
MA0115.10.874
MA0116.10.0383
MA0117.10.272
MA0119.10.838
MA0122.10.789
MA0124.10.744
MA0125.10.146
MA0131.10.237
MA0135.10.279
MA0136.11.52813e-4
MA0137.20.148
MA0138.20.0797
MA0139.10.86
MA0140.10.613
MA0141.10.249
MA0142.10.0179
MA0143.10.874
MA0144.10.305
MA0145.10.431
MA0146.10.218
MA0147.10.146
MA0148.10.532
MA0149.10.04
MA0150.10.696
MA0152.10.311
MA0153.10.643
MA0154.10.015
MA0155.10.31
MA0156.10.11
MA0157.10.447
MA0159.10.818
MA0160.10.443
MA0162.10.927
MA0163.10.15
MA0164.10.732
MA0258.10.0778
MA0259.10.139



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: CNhs11844

Novel motifP-value
10.729
100.589
1000.276
1010.392
1020.638
1030.338
1040.844
1050.541
1060.813
1070.695
1080.509
1090.341
110.195
1100.647
1110.734
1120.232
1130.149
1140.0937
1150.985
1160.528
1170.501
1180.572
1190.677
120.372
1200.757
1210.969
1220.439
1230.998
1240.0685
1250.961
1260.423
1270.989
1280.358
1290.719
130.0175
1300.157
1310.0485
1320.426
1330.00139
1340.00794
1350.03
1360.0203
1370.167
1380.594
1390.00416
140.475
1400.0823
1410.026
1420.826
1430.0405
1440.206
1450.64
1460.932
1470.992
1480.0426
1490.0505
150.431
1500.389
1510.464
1520.498
1530.643
1540.818
1550.451
1560.867
1570.506
1580.297
1590.269
160.995
1600.21
1610.673
1620.309
1630.597
1640.676
1650.541
1660.434
1670.402
1680.81
1690.747
170.471
180.204
190.0377
20.52
200.0929
210.867
220.372
230.0254
240.505
250.642
260.874
270.688
280.754
290.354
30.95
300.816
310.439
320.0144
330.121
340.143
350.00605
360.226
370.476
380.854
390.57
40.745
400.0402
410.181
420.825
430.149
440.864
450.872
460.162
470.498
480.938
490.141
50.164
500.25
510.756
520.857
530.593
540.439
550.341
560.994
570.623
580.252
590.114
60.942
600.423
610.869
620.0355
630.766
640.973
650.227
665.02115e-4
670.917
680.0913
690.938
70.87
700.0407
710.691
720.339
730.701
740.0659
750.349
760.866
770.491
780.271
790.266
80.798
800.0535
810.208
820.00698
830.332
840.634
850.00615
860.0949
870.0302
880.954
890.118
90.0213
900.309
910.0208
920.0419
930.572
940.129
950.148
960.0399
970.785
980.319
990.944



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: CNhs11844


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)

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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