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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,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: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: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: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:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120

Revision as of 16:42, 29 March 2012


Name:squamous cell lung carcinoma cell line:EBC-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age69
cell typeunclassifiable
cell lineEBC-1
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-0.024
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-lymphoma-0.0951
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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: CNhs11273

Jaspar motifP-value
MA0002.20.228
MA0003.10.109
MA0004.10.00861
MA0006.10.47
MA0007.10.284
MA0009.10.376
MA0014.10.0235
MA0017.10.387
MA0018.20.0589
MA0019.10.383
MA0024.10.279
MA0025.10.202
MA0027.10.632
MA0028.14.29364e-12
MA0029.10.969
MA0030.10.68
MA0031.10.653
MA0035.20.922
MA0038.10.152
MA0039.20.736
MA0040.10.445
MA0041.10.673
MA0042.10.858
MA0043.10.0296
MA0046.10.64
MA0047.20.119
MA0048.10.318
MA0050.10.289
MA0051.10.0394
MA0052.10.00601
MA0055.11.42746e-4
MA0057.10.684
MA0058.13.36652e-4
MA0059.10.0138
MA0060.10.546
MA0061.10.536
MA0062.25.1362e-15
MA0065.20.0531
MA0066.10.96
MA0067.10.557
MA0068.10.0529
MA0069.10.717
MA0070.10.171
MA0071.10.638
MA0072.10.338
MA0073.10.809
MA0074.10.814
MA0076.13.12865e-16
MA0077.10.804
MA0078.10.712
MA0079.20.0999
MA0080.20.00425
MA0081.10.617
MA0083.10.00152
MA0084.10.333
MA0087.10.999
MA0088.10.0425
MA0090.10.567
MA0091.10.0852
MA0092.10.671
MA0093.10.00373
MA0099.21.14219e-12
MA0100.10.446
MA0101.10.277
MA0102.20.291
MA0103.14.78557e-8
MA0104.29.6725e-4
MA0105.10.926
MA0106.10.281
MA0107.10.0688
MA0108.26.87685e-15
MA0111.10.505
MA0112.20.164
MA0113.10.505
MA0114.10.0144
MA0115.10.0625
MA0116.10.167
MA0117.10.906
MA0119.10.498
MA0122.10.853
MA0124.10.458
MA0125.10.434
MA0131.10.0754
MA0135.10.0491
MA0136.10.171
MA0137.20.118
MA0138.20.0908
MA0139.12.52766e-4
MA0140.10.438
MA0141.10.47
MA0142.10.948
MA0143.10.996
MA0144.10.508
MA0145.10.775
MA0146.10.819
MA0147.19.4274e-4
MA0148.10.00382
MA0149.10.0333
MA0150.11.5219e-5
MA0152.10.891
MA0153.10.106
MA0154.10.695
MA0155.10.0392
MA0156.12.80816e-4
MA0157.10.814
MA0159.10.00491
MA0160.10.143
MA0162.10.912
MA0163.10.00383
MA0164.10.173
MA0258.10.776
MA0259.10.0579



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: CNhs11273

Novel motifP-value
10.0706
100.0476
1000.0438
1010.633
1020.826
1030.173
1040.347
1050.514
1060.063
1070.176
1080.703
1090.021
110.997
1100.247
1110.0779
1120.954
1130.109
1140.134
1150.023
1160.225
1170.0183
1180.51
1190.0975
120.792
1200.124
1210.944
1220.309
1230.0256
1240.47
1250.637
1260.641
1270.632
1280.0168
1290.436
130.0171
1300.566
1310.235
1320.236
1330.122
1340.182
1350.063
1360.208
1370.488
1380.912
1390.274
140.799
1400.489
1410.37
1420.301
1430.0162
1440.0285
1450.574
1460.41
1470.997
1480.0511
1490.947
150.106
1500.781
1510.733
1520.231
1530.856
1540.941
1550.862
1560.495
1570.948
1580.888
1590.216
160.788
1600.388
1610.674
1620.893
1630.787
1640.0761
1650.428
1660.299
1670.0242
1680.61
1690.46
170.955
180.724
190.638
20.412
200.0624
210.342
220.575
230.148
240.0879
250.448
260.839
270.612
280.305
290.0402
30.407
300.535
310.365
320.0131
330.0739
340.102
350.498
360.0242
370.527
380.533
390.457
40.917
400.0215
410.491
420.219
430.71
440.52
450.635
460.895
470.313
480.535
490.984
50.66
500.705
510.908
520.146
530.747
540.717
550.866
560.928
570.351
580.983
590.404
60.545
600.578
610.302
620.705
630.343
640.937
650.397
660.119
670.905
680.0117
690.208
70.0738
700.0296
710.236
720.921
730.421
740.765
750.0116
760.0887
770.82
780.161
790.0546
80.665
800.573
810.477
820.523
830.538
840.684
850.327
860.462
870.0809
880.82
890.429
90.0919
900.176
910.885
920.588
930.836
940.901
950.201
960.788
970.723
980.501
990.066



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: CNhs11273


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)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
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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