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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000115,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000115,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|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 16:32, 29 March 2012


Name:epidermoid carcinoma cell line:A431
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuevulva
dev stage85 year old adult
sexfemale
age85
cell typeunclassifiable
cell lineA431
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-0.00591
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-lymphoma0.545
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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: CNhs10743

Jaspar motifP-value
MA0002.20.0331
MA0003.10.466
MA0004.10.607
MA0006.10.0998
MA0007.10.196
MA0009.10.227
MA0014.10.0961
MA0017.10.884
MA0018.20.704
MA0019.10.548
MA0024.11.30272e-5
MA0025.10.0102
MA0027.10.971
MA0028.10.222
MA0029.10.545
MA0030.10.00928
MA0031.10.105
MA0035.20.0589
MA0038.10.184
MA0039.22.41552e-4
MA0040.10.179
MA0041.10.849
MA0042.10.953
MA0043.10.505
MA0046.10.267
MA0047.20.105
MA0048.10.251
MA0050.11.22104e-4
MA0051.15.47206e-4
MA0052.10.435
MA0055.15.90627e-5
MA0057.10.185
MA0058.10.199
MA0059.10.184
MA0060.13.73957e-5
MA0061.10.838
MA0062.20.465
MA0065.20.381
MA0066.10.369
MA0067.10.445
MA0068.10.704
MA0069.10.793
MA0070.10.721
MA0071.10.372
MA0072.10.371
MA0073.10.745
MA0074.10.208
MA0076.10.42
MA0077.10.26
MA0078.10.765
MA0079.20.308
MA0080.20.00112
MA0081.10.135
MA0083.10.317
MA0084.10.07
MA0087.10.52
MA0088.10.822
MA0090.10.0392
MA0091.17.81161e-4
MA0092.10.207
MA0093.10.575
MA0099.29.18333e-13
MA0100.10.916
MA0101.10.293
MA0102.20.826
MA0103.12.04008e-7
MA0104.20.671
MA0105.10.0809
MA0106.16.35795e-4
MA0107.10.344
MA0108.20.0398
MA0111.10.627
MA0112.20.489
MA0113.10.66
MA0114.10.408
MA0115.10.581
MA0116.10.298
MA0117.10.439
MA0119.10.803
MA0122.10.87
MA0124.10.682
MA0125.10.0325
MA0131.10.55
MA0135.10.0861
MA0136.10.139
MA0137.20.859
MA0138.20.0336
MA0139.10.973
MA0140.10.485
MA0141.10.116
MA0142.10.0784
MA0143.10.92
MA0144.10.511
MA0145.10.228
MA0146.10.15
MA0147.10.537
MA0148.10.00959
MA0149.10.138
MA0150.10.414
MA0152.10.677
MA0153.10.613
MA0154.10.223
MA0155.10.37
MA0156.10.913
MA0157.10.462
MA0159.10.307
MA0160.10.776
MA0162.10.886
MA0163.10.0588
MA0164.10.591
MA0258.10.28
MA0259.10.69



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: CNhs10743

Novel motifP-value
10.922
100.551
1000.665
1010.446
1020.397
1030.423
1040.607
1050.23
1060.891
1070.422
1080.898
1090.00855
110.305
1100.645
1110.574
1120.482
1130.197
1140.207
1150.846
1160.0476
1170.456
1180.72
1190.309
120.807
1200.995
1210.399
1220.188
1230.782
1240.0764
1250.34
1260.996
1270.68
1280.288
1290.643
130.00429
1300.467
1310.588
1320.935
1330.0101
1340.28
1350.0104
1360.0237
1370.127
1380.878
1390.00253
140.771
1400.0569
1410.912
1420.487
1430.0117
1440.133
1450.863
1460.566
1470.674
1480.258
1490.045
150.373
1500.251
1510.888
1520.116
1530.873
1540.605
1550.732
1560.802
1570.853
1580.494
1590.836
160.807
1600.631
1610.95
1620.613
1630.796
1640.997
1650.941
1660.374
1670.572
1680.498
1690.222
170.372
180.295
190.0665
20.979
200.189
210.82
220.75
230.538
240.117
250.773
260.673
270.415
280.289
290.587
30.789
300.207
310.16
320.00151
330.227
340.58
350.00265
360.984
370.514
380.662
390.694
40.777
400.185
410.131
420.592
430.262
440.652
450.324
460.501
470.689
480.822
490.109
50.349
500.161
510.816
520.305
530.809
540.905
550.852
560.864
570.715
580.881
590.748
60.312
600.352
610.597
620.408
630.589
640.968
650.333
660.0574
670.713
680.0401
690.597
70.487
700.571
710.558
720.986
730.161
740.00309
750.325
760.814
770.826
780.103
791.43895e-4
80.468
800.167
810.0249
820.00232
830.887
840.962
850.0607
860.432
870.025
880.841
890.564
90.353
900.0478
910.0307
920.113
930.663
940.0433
950.106
960.114
970.655
980.144
990.345



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: CNhs10743


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)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000115 (lung epithelium)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
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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