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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006562,UBERON:0007026
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006562,UBERON:0007026
|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:0100819,FF:0101120
|fonse_cell_line=FF:0100819,FF:0101120
|fonse_cell_line_closure=FF:0100819,FF:0101120
|fonse_cell_line_closure=FF:0100819,FF:0101120

Revision as of 16:56, 29 March 2012


Name:pharyngeal carcinoma cell line:Detroit 562
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepharynx
dev stageNA
sexfemale
ageNA
cell typeunclassifiable
cell lineDetroit 562
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-penis0.332
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-lymphoma0.168
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11849

Jaspar motifP-value
MA0002.24.30045e-4
MA0003.10.603
MA0004.10.832
MA0006.10.0592
MA0007.10.414
MA0009.10.548
MA0014.10.11
MA0017.10.174
MA0018.20.0155
MA0019.10.535
MA0024.10.127
MA0025.10.66
MA0027.10.761
MA0028.10.89
MA0029.10.967
MA0030.10.137
MA0031.10.497
MA0035.20.579
MA0038.10.497
MA0039.20.159
MA0040.10.187
MA0041.10.878
MA0042.10.367
MA0043.10.522
MA0046.10.748
MA0047.20.111
MA0048.10.58
MA0050.13.09005e-6
MA0051.13.49539e-4
MA0052.10.107
MA0055.10.418
MA0057.10.6
MA0058.10.328
MA0059.10.0484
MA0060.10.624
MA0061.10.29
MA0062.20.0534
MA0065.20.224
MA0066.10.171
MA0067.10.212
MA0068.10.465
MA0069.10.244
MA0070.10.249
MA0071.10.004
MA0072.10.0204
MA0073.10.491
MA0074.10.926
MA0076.10.267
MA0077.10.0375
MA0078.10.717
MA0079.20.173
MA0080.21.67573e-4
MA0081.10.0139
MA0083.10.368
MA0084.10.8
MA0087.10.73
MA0088.10.0211
MA0090.11.87032e-4
MA0091.10.00107
MA0092.10.936
MA0093.10.689
MA0099.22.77815e-4
MA0100.10.377
MA0101.10.875
MA0102.20.188
MA0103.11.3889e-6
MA0104.20.0947
MA0105.14.14428e-4
MA0106.10.0316
MA0107.10.89
MA0108.20.0289
MA0111.10.694
MA0112.20.129
MA0113.10.101
MA0114.10.171
MA0115.10.576
MA0116.10.00483
MA0117.10.0128
MA0119.10.39
MA0122.10.795
MA0124.10.0855
MA0125.10.273
MA0131.10.638
MA0135.10.208
MA0136.10.00176
MA0137.20.22
MA0138.20.12
MA0139.10.775
MA0140.10.788
MA0141.10.0476
MA0142.10.0168
MA0143.10.158
MA0144.10.9
MA0145.10.969
MA0146.10.185
MA0147.10.0482
MA0148.10.0197
MA0149.10.311
MA0150.10.17
MA0152.10.233
MA0153.10.722
MA0154.10.00822
MA0155.10.606
MA0156.10.0312
MA0157.10.661
MA0159.10.0967
MA0160.10.0978
MA0162.10.808
MA0163.11.85987e-4
MA0164.10.397
MA0258.10.137
MA0259.10.495



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: CNhs11849

Novel motifP-value
10.164
100.422
1000.352
1010.884
1020.525
1030.565
1040.409
1050.826
1060.056
1070.00817
1080.686
1090.521
110.0931
1100.576
1110.778
1120.201
1130.654
1140.0415
1150.178
1160.462
1170.204
1180.157
1190.915
120.0579
1200.908
1210.208
1220.853
1230.804
1240.163
1250.883
1260.834
1270.696
1280.768
1290.754
130.55
1300.755
1310.663
1320.195
1330.426
1340.258
1350.586
1360.0122
1370.103
1380.961
1390.0949
140.98
1400.776
1410.249
1420.792
1438.87995e-4
1440.132
1450.632
1460.646
1470.0692
1480.665
1490.225
150.21
1500.27
1510.869
1520.00926
1530.583
1540.491
1550.694
1560.974
1570.813
1580.225
1590.977
160.772
1600.457
1610.37
1620.326
1630.928
1640.96
1650.665
1660.542
1670.933
1680.693
1690.345
170.82
180.164
190.0828
20.966
200.647
210.881
220.151
230.841
240.738
250.275
260.449
270.766
280.92
290.814
30.334
300.211
310.365
320.0315
330.289
340.353
350.0458
360.132
370.379
380.996
390.25
40.132
400.488
410.0236
420.63
430.0451
440.912
450.777
460.181
470.218
480.775
490.00728
50.68
500.696
510.49
520.253
530.471
540.637
550.233
560.746
570.915
580.625
590.237
60.912
600.165
610.569
620.156
630.883
640.701
650.725
660.685
670.233
680.0725
690.421
70.977
700.754
710.57
720.199
730.271
740.00744
750.713
760.802
770.863
780.726
790.465
80.237
800.0398
810.0618
820.00156
830.384
840.391
850.456
860.499
870.0606
880.424
890.901
90.144
900.417
910.165
920.56
930.797
940.145
950.672
960.0444
970.589
980.184
990.919



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: CNhs11849


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
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0006562 (pharynx)
0007026 (primitive gut)

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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